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==Lab Projects==
*[[Rui:RNAseq|RNAseq]]
*[[Rui:Methylome|Methylome]]
*[[Rui:DNAseq|DNAseq]]
*[[Rui:Pseudogenes|Pseudogenes]]
*[[Rui:Genelist|Neuronal gene list]]
*[[Rui:SingelCell|SingleCell RNAseq]]
*[[Rui:Data Analysis|Data Analysis]]
*[[Rui:Haplotying|Haplotying]]
*[[Rui:Samples-Calendar|Samples-Calendar]]
 


==Sample record for sequencing==
==Sample record for sequencing==
===colonyD and F samples for Hiseq===
'''RL-D2.P0_24-May15; RL-D3.P0_24-May15'''
D_p0:[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/DNA_Collaborations/2012-5-9] [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/DNA_Collaborations/2012-5-10]
'''RL-N/A-D/F_p5-Jun6'''
D/F_p5:[http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/DNA_Collaborations/2012-6-6]
===5.16.12 samples for Hiseq===
RL-KH-Tn5mC-May16
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''Label (cells)'''
| align="center" style="background:#f0f0f0;"|'''Cell #'''
| align="center" style="background:#f0f0f0;"|'''Label (Tn5mCseq)'''
| align="center" style="background:#f0f0f0;"|'''Primer'''
| align="center" style="background:#f0f0f0;"|'''Indx'''
| align="center" style="background:#f0f0f0;"|'''Label (pool)'''
| align="center" style="background:#f0f0f0;"|'''Seq Run'''
|-
| KH_Tn5mC_73||Female/Wt/Somatic(1)||4,342||KH_1_5.15.12||Nx||Indx73||RL-KH-Tn5mC-May16||Hiseq_Apr25
|-
| KH_Tn5mC_74||Female/Wt/Somatic(2)||3,906||KH_2_5.15.12||||Indx74||||6 lanes
|-
| KH_Tn5mC_75||Female/Wt/PGC(1)||3,728||KH_3_5.15.12||||Indx75||||
|-
| KH_Tn5mC_77||Female/homo/Somatic(1)||4,291||KH_5_5.15.12||||Indx77||||
|-
| KH_Tn5mC_78||Female/homo/Somatic(2)||4,254||KH_6_5.15.12||||Indx78||||
|-
| KH_Tn5mC_79||Female/homo/PGC(1)||3,266||KH_7_5.15.12||||Indx79||||
|-
| KH_Tn5mC_80||Female/homo/PGC(2)||4,700||KH_8_5.15.12||||Indx80||||
|-
| A3_Tn5mC_86||dFib_iPSC_A3p0||unknown||An_A3_5.15.12||Nx||Indx86||||
|-
| ||||||||||||||
|-
| KH_Tn5mC_76||Female/Wt/PGC(2)||1,575||KH_4_5.15.12||||Indx76||||HL119
|}
===5.2.12 samples for Hiseq===
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''Template'''
| align="center" style="background:#f0f0f0;"|'''DNA'''
| align="center" style="background:#f0f0f0;"|'''Prmier'''
| align="center" style="background:#f0f0f0;"|'''Index'''
| align="center" style="background:#f0f0f0;"|'''Label in strip'''
| align="center" style="background:#f0f0f0;"|'''Label (pool)'''
|-
| D-p15_Indx73||D-p15||5ng||Nextera||Indx73||D1||RL_dFB_D-p15_24_5.2.12
|-
| D-p15_Indx74||5ng/ul||||||Indx74||D1||
|-
| D-p15_Indx75||||||||Indx75||D1||
|-
| D-p15_Indx76||||||||Indx76||D1||
|-
| D-p15_Indx77||||||||Indx77||D1||
|-
| D-p15_Indx78||||||||Indx78||D1||
|-
| D-p15_Indx79||||||||Indx79||D1||
|-
| D-p15_Indx80||||||||Indx80||D1||
|-
| D-p15_Indx81||||||||Indx81||D2||
|-
| D-p15_Indx82||||||||Indx82||D2||
|-
| D-p15_Indx83||||||||Indx83||D2||
|-
| D-p15_Indx84||||||||Indx84||D2||
|-
| D-p15_Indx85||||||||Indx85||D2||
|-
| D-p15_Indx86||||||||Indx86||D2||
|-
| D-p15_Indx87||||||||Indx87||D2||
|-
| D-p15_Indx88||||||||Indx88||D2||
|-
| D-p15_Indx89||||||||Indx89||D3||
|-
| D-p15_Indx90||||||||Indx90||D3||
|-
| D-p15_Indx91||||||||Indx91||D3||
|-
| D-p15_Indx92||||||||Indx92||D3||
|-
| D-p15_Indx93||||||||Indx93||D3||
|-
| D-p15_Indx94||||||||Indx94||D3||
|-
| D-p15_Indx95||||||||Indx95||D3||
|-
| D-p15_Indx96||||||||Indx96||D3||
|}
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''Template'''
| align="center" style="background:#f0f0f0;"|'''DNA'''
| align="center" style="background:#f0f0f0;"|'''Prmier'''
| align="center" style="background:#f0f0f0;"|'''Index'''
| align="center" style="background:#f0f0f0;"|'''Label in strip'''
| align="center" style="background:#f0f0f0;"|'''Label (pool)'''
|-
| F-p15_Indx73||F-p15||5ng||Nextera||Indx73||F1||RL_dFB_F-p15_24_5.2.12
|-
| F-p15_Indx74||5ng/ul||||||Indx74||F1||
|-
| F-p15_Indx75||||||||Indx75||F1||
|-
| F-p15_Indx76||||||||Indx76||F1||
|-
| F-p15_Indx77||||||||Indx77||F1||
|-
| F-p15_Indx78||||||||Indx78||F1||
|-
| F-p15_Indx79||||||||Indx79||F1||
|-
| F-p15_Indx80||||||||Indx80||F1||
|-
| F-p15_Indx81||||||||Indx81||F2||
|-
| F-p15_Indx82||||||||Indx82||F2||
|-
| F-p15_Indx83||||||||Indx83||F2||
|-
| F-p15_Indx84||||||||Indx84||F2||
|-
| F-p15_Indx85||||||||Indx85||F2||
|-
| F-p15_Indx86||||||||Indx86||F2||
|-
| F-p15_Indx87||||||||Indx87||F2||
|-
| F-p15_Indx88||||||||Indx88||F2||
|-
| F-p15_Indx89||||||||Indx89||F3||
|-
| F-p15_Indx90||||||||Indx90||F3||
|-
| F-p15_Indx91||||||||Indx91||F3||
|-
| F-p15_Indx92||||||||Indx92||F3||
|-
| F-p15_Indx93||||||||Indx93||F3||
|-
| F-p15_Indx94||||||||Indx94||F3||
|-
| F-p15_Indx95||||||||Indx95||F3||
|-
| F-p15_Indx96||||||||Indx96||F3||
|}
===4.24.12 samples for HL118/Hiseq===
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''Label (cells)'''
| align="center" style="background:#f0f0f0;"|'''Cell #'''
| align="center" style="background:#f0f0f0;"|'''Label (RNAseq)'''
| align="center" style="background:#f0f0f0;"|'''Primer'''
| align="center" style="background:#f0f0f0;"|'''Indx'''
| align="center" style="background:#f0f0f0;"|'''Label (pool)'''
| align="center" style="background:#f0f0f0;"|'''Seq Run'''
|-
| ES1||H9/45 ES, 11/4/11||1000||wei#1_4.9.12||illumina N2 ||Indx73||RL_wei1-12_4.10.12||Hiseq_
|-
| ES2||H9/50 ES, 11/28||1000||wei#2_4.9.12||||Indx74||||1 lane
|-
| DE1||H9/41 DE, 10/20||1000||wei#3_4.9.12||||Indx75||||
|-
| DE2||H9/46f DE, 10/31||1000||wei#4_4.9.12||||Indx76||||
|-
| PP1||S3/f, 10/14||1000||wei#5_4.9.12||||Indx77||||
|-
| PP2||S3/f P2, 10/14||1000||wei#6_4.9.12||||Indx78||||
|-
| PP3||62M, 24+, 10/26||1000||wei#7_4.9.12||||Indx79||||
|-
| a1||alpha, 11/17||1000||wei#8_4.9.12||||Indx80||||
|-
| a2||alpha, 11/11||1000||wei#9_4.9.12||||Indx81||||
|-
| b1||beta, 11/17||1000||wei#10_4.9.12||||Indx82||||
|-
| b2||beta, 11/11||1000||wei#11_4.9.12||||Indx83||||
|-
| Px||Px+, 11/17||1000||wei#12_4.9.12||||Indx84||||
|}
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''Label (strip)'''
| align="center" style="background:#f0f0f0;"|'''re-mix (ul)'''
| align="center" style="background:#f0f0f0;"|'''primer'''
| align="center" style="background:#f0f0f0;"|'''Indx'''
| align="center" style="background:#f0f0f0;"|'''Label (pool)'''
| align="center" style="background:#f0f0f0;"|'''Seq Run'''
|-
| B2_Indx73||B2_1A||1.49||Nextera||Indx73||RL_4.24.12_B2(remix)-23||HiSeq_
|-
| B2_Indx74||B2_1B||2.25||||Indx74||||2 lanes
|-
| B2_Indx75||B2_1C||0.98||||Indx75||||
|-
| B2_Indx76||B2_1D||1.08||||Indx76||||
|-
| B2_Indx77||B2_1E||1.34||||Indx77||||
|-
| B2_Indx78||B2_1F||1.11||||Indx78||||
|-
| B2_Indx79||B2_1G||1.06||||Indx79||||
|-
| B2_Indx80||B2_1H||1.61||||Indx80||||
|-
| B2_Indx81||B2_2A||1.41||||Indx81||||
|-
| B2_Indx82||B2_2B||1.15||||Indx82||||
|-
| B2_Indx83||B2_2C||1.05||||Indx83||||
|-
| B2_Indx84||B2_2D||0.92||||Indx84||||
|-
| B2_Indx85||B2_2E||1.60||||Indx85||||
|-
| B2_Indx86||B2_2F||1.09||||Indx86||||
|-
| B2_Indx87||B2_2G||2.08||||Indx87||||
|-
| B2_Indx88||B2_2H||1.69||||Indx88||||
|-
| B2_Indx89||B2_3A||10.00||||Indx89||||
|-
| B2_Indx90||B2_3B||1.07||||Indx90||||
|-
| B2_Indx91||B2_3C||0.88||||Indx91||||
|-
| B2_Indx92||B2_3D||1.36||||Indx92||||
|-
| B2_Indx93||B2_3E||3.00||||Indx93||||
|-
| B2_Indx94||B2_3F||1.80||||Indx94||||
|-
| B2_Indx95||B2_3G||1.23||||Indx95||||
|-
| ||||||||||||
|-
| B3_Indx73||B3_1A||3||Nextera||Indx73||RL_4.24.12_B3(remix)-23||HiSeq_
|-
| B3_Indx74||B3_1B||1.49||||Indx74||||2 lanes
|-
| B3_Indx75||B3_1C||0.86||||Indx75||||
|-
| B3_Indx76||B3_1D||1.52||||Indx76||||
|-
| B3_Indx77||B3_1E||1.66||||Indx77||||
|-
| B3_Indx78||B3_1F||1.72||||Indx78||||
|-
| B3_Indx79||B3_1G||2.04||||Indx79||||
|-
| B3_Indx80||B3_1H||1.95||||Indx80||||
|-
| B3_Indx81||B3_2A||1.48||||Indx81||||
|-
| B3_Indx82||B3_2B||1.28||||Indx82||||
|-
| B3_Indx83||B3_2C||1.31||||Indx83||||
|-
| B3_Indx84||B3_2D||1.78||||Indx84||||
|-
| B3_Indx85||B3_2E||1.82||||Indx85||||
|-
| B3_Indx86||B3_2F||1.51||||Indx86||||
|-
| B3_Indx87||B3_2G||1.17||||Indx87||||
|-
| B3_Indx88||B3_2H||1.01||||Indx88||||
|-
| B3_Indx90||B3_3B||1.57||||Indx90||||
|-
| B3_Indx91||B3_3C||2.35||||Indx91||||
|-
| B3_Indx92||B3_3D||1.94||||Indx92||||
|-
| B3_Indx93||B3_3E||1.22||||Indx93||||
|-
| B3_Indx94||B3_3F||1.66||||Indx94||||
|-
| B3_Indx95||B3_3G||1.14||||Indx95||||
|-
| B3_Indx96||B3_3H||1.43||||Indx96||||
|}
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|''''''
| align="center" style="background:#f0f0f0;"|'''Label (cells)'''
| align="center" style="background:#f0f0f0;"|'''DNA'''
| align="center" style="background:#f0f0f0;"|'''Prmier'''
| align="center" style="background:#f0f0f0;"|'''Index'''
| align="center" style="background:#f0f0f0;"|'''Label in strip'''
| align="center" style="background:#f0f0f0;"|'''Nextera Indx'''
| align="center" style="background:#f0f0f0;"|'''Label (pool)'''
|-
| Fib_Indx73||Fib_bulk||6ng||Nextera||Indx73||F1||RL_4.24.12_FIB-24||HiSeq_
|-
| Fib_Indx74||6ng/ul||||||Indx74||F1||||1 lanes
|-
| Fib_Indx75||||||||Indx75||F1||||
|-
| Fib_Indx76||||||||Indx76||F1||||
|-
| Fib_Indx77||||||||Indx77||F1||||
|-
| Fib_Indx78||||||||Indx78||F1||||
|-
| Fib_Indx79||||||||Indx79||F1||||
|-
| Fib_Indx80||||||||Indx80||F1||||
|-
| Fib_Indx81||||||||Indx81||F2||||
|-
| Fib_Indx82||||||||Indx82||F2||||
|-
| Fib_Indx83||||||||Indx83||F2||||
|-
| Fib_Indx84||||||||Indx84||F2||||
|-
| Fib_Indx85||||||||Indx85||F2||||
|-
| Fib_Indx86||||||||Indx86||F2||||
|-
| Fib_Indx87||||||||Indx87||F2||||
|-
| Fib_Indx88||||||||Indx88||F2||||
|-
| Fib_Indx89||||||||Indx89||F3||||
|-
| Fib_Indx90||||||||Indx90||F3||||
|-
| Fib_Indx91||||||||Indx91||F3||||
|-
| Fib_Indx92||||||||Indx92||F3||||
|-
| Fib_Indx93||||||||Indx93||F3||||
|-
| Fib_Indx94||||||||Indx94||F3||||
|-
| Fib_Indx95||||||||Indx95||F3||||
|-
| Fib_Indx96||||||||Indx96||F3||||
|-
| ||||||||||||||
|-
| B-P30_Indx73||dFB_B_P30||5ng||Nextera||Indx73||P30-1||RL_4.24.12_B-P30-24||HiSeq_
|-
| B-P30_Indx74||5ng/ul||||||Indx74||P30-1||||2 lanes
|-
| B-P30_Indx75||||||||Indx75||P30-1||||
|-
| B-P30_Indx76||||||||Indx76||P30-1||||
|-
| B-P30_Indx77||||||||Indx77||P30-1||||
|-
| B-P30_Indx78||||||||Indx78||P30-1||||
|-
| B-P30_Indx79||||||||Indx79||P30-1||||
|-
| B-P30_Indx80||||||||Indx80||P30-1||||
|-
| B-P30_Indx81||||||||Indx81||P30-2||||
|-
| B-P30_Indx82||||||||Indx82||P30-2||||
|-
| B-P30_Indx83||||||||Indx83||P30-2||||
|-
| B-P30_Indx84||||||||Indx84||P30-2||||
|-
| B-P30_Indx85||||||||Indx85||P30-2||||
|-
| B-P30_Indx86||||||||Indx86||P30-2||||
|-
| B-P30_Indx87||||||||Indx87||P30-2||||
|-
| B-P30_Indx88||||||||Indx88||P30-2||||
|-
| B-P30_Indx89||||||||Indx89||P30-3||||
|-
| B-P30_Indx90||||||||Indx90||P30-3||||
|-
| B-P30_Indx91||||||||Indx91||P30-3||||
|-
| B-P30_Indx92||||||||Indx92||P30-3||||
|-
| B-P30_Indx93||||||||Indx93||P30-3||||
|-
| B-P30_Indx94||||||||Indx94||P30-3||||
|-
| B-P30_Indx95||||||||Indx95||P30-3||||
|-
| B-P30_Indx96||||||||Indx96||P30-3||||
|}
===3.8.12 sample for HiSeq_120313===
'''RL_B2_23s_Mar8.2012'''
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|'''Sample ID'''
| align="center" style="background:#f0f0f0;"|'''Index'''
| align="center" style="background:#f0f0f0;"|'''Adapter'''
|-
| B2-1||Indx73||Nextera
|-
| B2-2||Indx74||Nextera
|-
| B2-3||Indx75||Nextera
|-
| B2-4||Indx76||Nextera
|-
| B2-5||Indx77||Nextera
|-
| B2-6||Indx78||Nextera
|-
| B2-7||Indx79||Nextera
|-
| B2-8||Indx80||Nextera
|-
| B2-9||Indx81||Nextera
|-
| B2-10||Indx82||Nextera
|-
| B2-11||Indx83||Nextera
|-
| B2-12||Indx84||Nextera
|-
| B2-13||Indx85||Nextera
|-
| B2-14||Indx86||Nextera
|-
| B2-15||Indx87||Nextera
|-
| B2-16||Indx88||Nextera
|-
| B2-17||Indx89||Nextera
|-
| B2-18||Indx90||Nextera
|-
| B2-19||Indx91||Nextera
|-
| B2-20||Indx92||Nextera
|-
| B2-21||Indx93||Nextera
|-
| B2-22||Indx94||Nextera
|-
| B2-23||Indx95||Nextera
|-
|
|}
'''RL_B3_24s_Mar8.2012'''
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|'''Sample ID'''
| align="center" style="background:#f0f0f0;"|'''Index'''
| align="center" style="background:#f0f0f0;"|'''Adapter'''
|-
| B3-1||Indx73||Nextera
|-
| B3-2||Indx74||Nextera
|-
| B3-3||Indx75||Nextera
|-
| B3-4||Indx76||Nextera
|-
| B3-5||Indx77||Nextera
|-
| B3-6||Indx78||Nextera
|-
| B3-7||Indx79||Nextera
|-
| B3-8||Indx80||Nextera
|-
| B3-9||Indx81||Nextera
|-
| B3-10||Indx82||Nextera
|-
| B3-11||Indx83||Nextera
|-
| B3-12||Indx84||Nextera
|-
| B3-13||Indx85||Nextera
|-
| B3-14||Indx86||Nextera
|-
| B3-15||Indx87||Nextera
|-
| B3-16||Indx88||Nextera
|-
| B3-17||Indx89||Nextera
|-
| B3-18||Indx90||Nextera
|-
| B3-19||Indx91||Nextera
|-
| B3-20||Indx92||Nextera
|-
| B3-21||Indx93||Nextera
|-
| B3-22||Indx94||Nextera
|-
| B3-23||Indx95||Nextera
|-
| B3-24||Indx96||Nextera
|-
|
|}


6.8.11: '''RL-Hap_RNAseq-1_13-Jun6'''
'''RL_Fib-Bulk_Mar8.2012''': Indx96, Nextera
 
 
Lab note: B2 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/DNA_Collaborations/2012-3-2] B3 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/DNA_Collaborations/2012-3-5] Fib-bulk [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/DNA_Collaborations/2012-3-7]
 
Final gel check: 1, 3, 4 lanes in this link [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/DNA_Collaborations/2012-3-8]
 
===1.31.12 sample for HL114===
'''RL_Fib100c_29s_ExoCap_Jan31.2012''' (L2, L3)
Lab note: [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/DNA_Collaborations/2012-1-5] [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/DNA_Collaborations/2012-1-31]
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|'''ID'''
| align="center" style="background:#f0f0f0;"|'''Sample'''
| align="center" style="background:#f0f0f0;"|'''MDA'''
| align="center" style="background:#f0f0f0;"|'''Index'''
|-
| U-1||Human||MM||Indx73
|-
| U-2||Fibroblast||MM||Indx74
|-
| U-3||100c||MM||Indx75
|-
| U-4||||MM||Indx76
|-
| U-5||~5c/well||MM||Indx77
|-
| U-6||MDA 1.5hrs||MM||Indx78
|-
| U-7||||MM||Indx79
|-
| U-8||Tn-I PCR||MM||Indx80
|-
| U-9||||MM||Indx81
|-
| U-10||900ng for||MM||Indx82
|-
| U-11||ExoCap||MM||Indx83
|-
| U-12||||MM||Indx84
|-
| U-13||||MM||Indx85
|-
| U-14||||MM||Indx86
|-
| U-15||||MM||Indx87
|-
| U-16||||MM||Indx88
|-
| A1-2||||Aliquot-cool||Indx90
|-
| A1-3||||Aliquot-cool||Indx91
|-
| A1-4||||Aliquot-cool||Indx92
|-
| A1-5||||Aliquot-cool||Indx93
|-
| A1-6||||Aliquot-cool||Indx94
|-
| A1-7||||Aliquot-cool||Indx95
|-
| A1-8||||Aliquot-cool||Indx96
|-
| A2-3||||Aliquot-RT||Indx3
|-
| A2-4||||Aliquot-RT||Indx4
|-
| A2-5||||Aliquot-RT||Indx5
|-
| A2-6||||Aliquot-RT||Indx6
|-
| A2-7||||Aliquot-RT||Indx7
|-
| A2-8||||Aliquot-RT||Indx8
|}
 
'''RL_EF_ExoCap_Jan31.2012''' (L7)
Lab note: [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/DNA_Collaborations/2012-1-27] [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/DNA_Collaborations/2012-1-31]
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|'''ID'''
| align="center" style="background:#f0f0f0;"|'''Sample'''
| align="center" style="background:#f0f0f0;"|'''Method'''
| align="center" style="background:#f0f0f0;"|'''Index'''
|-
| ES||hES||Tn-I PCR||Indx1
|-
| Fib||hFibroblast||ExoCap||Indx2
|}
 
===HL113 and HiSeqFeb09===
HiSeqFeb09: ru-mix samples based on read ratio in HL113, HiSeqFeb09 L1-3
 
Lab note: [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/DNA_Collaborations/2011-12-20]
RL_BAC_73-96_12.22.11
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|'''A1'''
| align="center" style="background:#f0f0f0;"|'''Indx73'''
| align="center" style="background:#f0f0f0;"|'''Nextera'''
|-
| B1||Indx74||Nextera
|-
| C1||Indx75||Nextera
|-
| D1||Indx76||Nextera
|-
| E1||Indx77||Nextera
|-
| F1||Indx78||Nextera
|-
| G1||Indx79||Nextera
|-
| A2||Indx81||Nextera
|-
| B2||Indx82||Nextera
|-
| C2||Indx83||Nextera
|-
| D2||Indx84||Nextera
|-
| E2||Indx85||Nextera
|-
| F2||Indx86||Nextera
|-
| G2||Indx87||Nextera
|-
| H2||Indx88||Nextera
|-
| B3||Indx90||Nextera
|-
| C3||Indx91||Nextera
|-
| D3||Indx92||Nextera
|-
| E3||Indx93||Nextera
|-
| F3||Indx94||Nextera
|-
| G3||Indx95||Nextera
|-
| H3||Indx96||Nextera
|-
|
|}
 
===HL108===
* Haplotyping samples from new protocol - MDA followed by Nextera
* Lab note on 11.3.11 and 11.4.11 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Haplotyping/2011-11-3][http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Haplotyping/2011-11-4]
* Finally hap library including Indx73-80
 
RL-Hap-73_80-Nov8 [RL_hap_Indx73-80_11.8.11 in tube label]
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|'''Sample ID'''
| align="center" style="background:#f0f0f0;"|'''Source'''
| align="center" style="background:#f0f0f0;"|'''Genome'''
| align="center" style="background:#f0f0f0;"|'''IndX'''
|-
| Hap1||GM12878-p15, MDA 17ct-2||human||GA-Indx73
|-
| Hap2||GM12878-p15, MDA 22ct-3||''||GA-Indx74
|-
| Hap3||GM12878-p15, MDA 27ct-3||''||GA-Indx75
|-''
| Hap4||GM12878-p15, MDA 27ct-4||''||GA-Indx76
|-
| Hap5||GM12878-p15, MDA 30ct-1||''||GA-Indx77
|-
| Hap6||GM12878-p15, MDA 30ct-2||''||GA-Indx78
|-
| Hap7||GM12878-p15, MDA 30ct-3||''||GA-Indx79
|-
| Hap8||GM12878-p15, MDA 30ct-4||''||GA-Indx80
|}
 
===HL106/HL109===
* RNA libraries for Dr. Yi Zhang and Dr. Xu Yang lab
* The library probably has over-amplified issue, which may have more clonal reads [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-10-13#Final_gel_check]
* Complete notes for RNAseq libraries are from 10.3.11-10.8.11 (cDNA) and 10.11.11-10.13.11 (libraries)
* Final gel check [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-10-13#Mixed_RNAseq_libaries]
 
RL_RNAseq_Indx88-96_10.18.11
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|'''Sample'''
| align="center" style="background:#f0f0f0;"|'''Source'''
| align="center" style="background:#f0f0f0;"|'''Genome'''
| align="center" style="background:#f0f0f0;"|'''Index'''
| align="center" style="background:#f0f0f0;"|''''''
|-
| Ctrl-0d||Yi Zhang||Human||PCR_R.N2.Indx88||
|-
| B1-0d||Yi Zhang||Human||PCR_R.N2.Indx89||
|-
| B3-0d||Yi Zhang||Human||PCR_R.N2.Indx90||
|-
| Ctrl-2d||Yi Zhang||Human||PCR_R.N2.Indx91||
|-
| B1-2d||Yi Zhang||Human||PCR_R.N2.Indx92||
|-
| B3-2d||Yi Zhang||Human||PCR_R.N2.Indx93||
|-
| Ctrl||Xu Yang||Human||PCR_R.N2.Indx94||
|-
| RFP||Xu Yang||Human||PCR_R.N2.Indx95||
|-
| GFP+RFP||Xu Yang||Human||PCR_R.N2.Indx96||
|}
 
===HL101===
====Haplotyping samples====
# Lyse the cell aliquot #1 (10 cells) in 60 lysis buffer, aliquot 1ul cell lysates to 24 tubes and process with Nextera haplotyping protocol. Barcode the first 12 cell lysates with Nextera 1-12 as RL_hap1-12; barcode the second 12 cell lysates with Nextera 1-12 as RL_12-23 (w/o lysate #21). Individual hap samples were made on 8.23.11 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Haplotyping/2011-8-23] and size selection of pooled samples were made by Matt
# Lyse the cell aliquot #2 (10 cells) in 60 lysis buffer, aliquot 1ul cell lysates to 12 tubes and process with Nextera haplotyping protocol. Barcode the 12 cell lysates with Nextera 1-12 as MC_hap1-11 (w/o lysate #6). Individual hap samples were made by Matt on 8.24.11 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Haplotyping/2011-8-24] and size selection of pooled samples were made by Matt
# Final check on 9.2.11 lab note [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-9-2]
 
RL_hap1-12_9.2.11
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|'''Sample ID'''
| align="center" style="background:#f0f0f0;"|'''Source'''
| align="center" style="background:#f0f0f0;"|'''Genome'''
| align="center" style="background:#f0f0f0;"|'''IndX'''
|-
| Hap1||GM12878-p15, cell aliquot #1, lysate #1||human||Nextera ID1
|-
| Hap2||GM12878-p15, cell aliquot #1, lysate #2||''||Nextera ID2
|-
| Hap3||GM12878-p15, cell aliquot #1, lysate #3||''||Nextera ID3
|-''
| Hap4||GM12878-p15, cell aliquot #1, lysate #4||''||Nextera ID4
|-
| Hap5||GM12878-p15, cell aliquot #1, lysate #5||''||Nextera ID5
|-
| Hap6||GM12878-p15, cell aliquot #1, lysate #6||''||Nextera ID6
|-
| Hap7||GM12878-p15, cell aliquot #1, lysate #7||''||Nextera ID7
|-
| Hap8||GM12878-p15, cell aliquot #1, lysate #8||''||Nextera ID8
|-
| Hap9||GM12878-p15, cell aliquot #1, lysate #9||''||Nextera ID9
|-
| Hap10||GM12878-p15, cell aliquot #1, lysate #10||''||Nextera ID10
|-
| Hap11||GM12878-p15, cell aliquot #1, lysate #11||''||Nextera ID11
|-
| Hap12||GM12878-p15, cell aliquot #1, lysate #12||''||Nextera ID12
|}
 
RL_hap13-23_9.2.11
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|'''Sample ID'''
| align="center" style="background:#f0f0f0;"|'''Source'''
| align="center" style="background:#f0f0f0;"|'''Genome'''
| align="center" style="background:#f0f0f0;"|'''IndX'''
|-
| Hap13||GM12878-p15, cell aliquot #1, lysate #13||human||Nextera ID1
|-
| Hap14||GM12878-p15, cell aliquot #1, lysate #14||''||Nextera ID2
|-
| Hap15||GM12878-p15, cell aliquot #1, lysate #15||''||Nextera ID3
|-''
| Hap16||GM12878-p15, cell aliquot #1, lysate #16||''||Nextera ID4
|-
| Hap17||GM12878-p15, cell aliquot #1, lysate #17||''||Nextera ID5
|-
| Hap18||GM12878-p15, cell aliquot #1, lysate #18||''||Nextera ID6
|-
| Hap19||GM12878-p15, cell aliquot #1, lysate #19||''||Nextera ID7
|-
| Hap20||GM12878-p15, cell aliquot #1, lysate #20||''||Nextera ID8
|-
| Hap21||GM12878-p15, cell aliquot #1, lysate #22||''||Nextera ID10
|-
| Hap22||GM12878-p15, cell aliquot #1, lysate #23||''||Nextera ID11
|-
| Hap23||GM12878-p15, cell aliquot #1, lysate #24||''||Nextera ID12
|}


MC_hap1-11_9.2.11
{| {{table}} border=1
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|'''Sample ID'''
| align="center" style="background:#f0f0f0;"|'''Sample ID'''
| align="center" style="background:#f0f0f0;"|'''Source'''
| align="center" style="background:#f0f0f0;"|'''Genome'''
| align="center" style="background:#f0f0f0;"|'''Genome'''
| align="center" style="background:#f0f0f0;"|'''IndX'''
| align="center" style="background:#f0f0f0;"|'''IndX'''
|-
|-
| Hap1||human||Nextera ID1
| Hap1||GM12878-p15, cell aliquot #2, lysate #1||human||Nextera ID1
|-
| Hap2||GM12878-p15, cell aliquot #2, lysate #2||''||Nextera ID2
|-
| Hap3||GM12878-p15, cell aliquot #2, lysate #3||''||Nextera ID3
|-''
| Hap4||GM12878-p15, cell aliquot #2, lysate #4||''||Nextera ID4
|-
| Hap5||GM12878-p15, cell aliquot #2, lysate #5||''||Nextera ID5
|-
| Hap6||GM12878-p15, cell aliquot #2, lysate #7||''||Nextera ID7
|-
| Hap7||GM12878-p15, cell aliquot #2, lysate #8||''||Nextera ID8
|-
| Hap8||GM12878-p15, cell aliquot #2, lysate #9||''||Nextera ID9
|-
| Hap9||GM12878-p15, cell aliquot #2, lysate #10||''||Nextera ID10
|-
| Hap10||GM12878-p15, cell aliquot #2, lysate #11||''||Nextera ID11
|-
| Hap11||GM12878-p15, cell aliquot #2, lysate #12||''||Nextera ID12
|}
 
====RNA libraries for Dr. Yi Zhang lab====
# E9.5 (Indx3), E11.5 (Indx4), E13.5m1 (Indx5), and E13.5f1 (Indx6) are from amplified RNAs on lab note 7.11.11 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-7-11] and re-amplify with the rest of N2 adapter-ligated products on 9.1.11 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-9-1#Re-amplify_RNA_libraries_on_7.2F12.2F11]
# E9.5 (Indx7), E11.5 (Indx8), KO E13.5m (Indx13), KO E13.5f1 (Indx14), and KO E13.5f2 (Indx15) samples are from amplified RNAs on lab note 8.30.11 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-8-30]
# E13.5m1 (Indx9), E13.5m2 (Indx10), E13.5f1 (Indx11), and E13.5f2 (Indx12) are from amplified RNAs on lab note 8.31.11 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-8-31]
# spike-in RNA amount = (total amount of each sample X 8) / 10,000 (based on Dr. Zhang's assumption) for samples in No.2 and No.3 on lab note 8.31.11 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-8-31]
# Libraries processing is on lab note 8.31.11 and 9.1.11 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-8-31][http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-9-1]
# Final check in on lab note 9.2.11 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-9-2]
 
RL_RNAIndx7-15_9.2.11
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|'''Sample'''
| align="center" style="background:#f0f0f0;"|'''Source'''
| align="center" style="background:#f0f0f0;"|'''Barcode'''
|-
| E9.5||Mouse||PCR_R.N2Ind3
|-
|-
| Hap2||human||Nextera ID2
| E11.5||||PCR_R.N2Ind4
|-
|-
| Hap3||human||Nextera ID3
| wt E13.5m1||||PCR_R.N2Ind5
|-
|-
| Hap4||human||Nextera ID4
| wt E13.5f1||||PCR_R.N2Ind6
|-
|-
| Hap5||human||Nextera ID5
| E9.5||+ spike-in RNAs||PCR_R.N2Ind7
|-
|-
| Hap6||human||Nextera ID6
| E11.5||+ spike-in RNAs||PCR_R.N2Ind8
|-
|-
| Hap7||human||Nextera ID7
| wt E13.5m1||+ spike-in RNAs||PCR_R.N2Ind9
|-
|-
| Hap8||human||Nextera ID8
| wt E13.5m2||+ spike-in RNAs||PCR_R.N2Ind10
|-
|-
| Hap9||human||Nextera ID9
| wt E13.5f1||+ spike-in RNAs||PCR_R.N2Ind11
|-
|-
| Hap10||human||Nextera ID10
| wt E13.5f2||+ spike-in RNAs||PCR_R.N2Ind12
|-
|-
| Hap11||human||Nextera ID11
| KO E13.5m||+ spike-in RNAs||PCR_R.N2Ind13
|-
|-
| Hap12||human||Nextera ID12
| KO E13.5f1||+ spike-in RNAs||PCR_R.N2Ind14
|-
|-
| RNA-EL||mouse||PCR_R.N2Ind12
| KO E13.5f2||+ spike-in RNAs||PCR_R.N2Ind15
|-
|-
| RNA-ER||mouse||PCR_R.N2Ind13
|  
|}
|}


===HL099===
7.25.11: '''RL-RNAseq-1_4-July25'''


Hap samples (1-12) prepared on lab note 6.6.11 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Haplotyping/2011-6-6#2nd_round_of_PCR]. Briefly, Twelve cell lysate aliquots (~1pg gDNA) were amplified with Nextera adapter mix (barcode 1-12) and mixed the 12 samples at 1:1 ratio.
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|'''Sample'''
| align="center" style="background:#f0f0f0;"|'''Original volume'''
| align="center" style="background:#f0f0f0;"|'''Mappable reads'''
| align="center" style="background:#f0f0f0;"|'''Modified volume'''
| align="center" style="background:#f0f0f0;"|'''IndX'''
|-
| GFP+||2.55||0.8M||5.1||PCR_R.N2Ind1
|-
| GFP-||2||1.6M||2||PCR_R.N2Ind2
|-
| E9.5||3.04||1.5M||3.3||PCR_R.N2Ind3
|-
| E11.5||2.39||1.2M||3.18||PCR_R.N2Ind4
|}
 
 
===HL098===
7.13.11: '''RL-RNAseq-1_6-July12'''
 
{| {{table}} border=1
| align="center" style="background:#f0f0f0;"|'''Sample ID'''
| align="center" style="background:#f0f0f0;"|'''Source'''
| align="center" style="background:#f0f0f0;"|'''Genome'''
| align="center" style="background:#f0f0f0;"|'''IndX'''
|-
| GFP+||Xu Yang lab||human||PCR_R.N2Ind1
|-
| GFP-||Xu Yang lab||human||PCR_R.N2Ind2
|-
| E9.5||Yi Zhang lab||mouse||PCR_R.N2Ind3
|-
| E11.5||Yi Zhang lab||mouse||PCR_R.N2Ind4
|-
| E13.5m||Yi Zhang lab||mouse||PCR_R.N2Ind5
|-
| E13.5f||Yi Zhang lab||mouse||PCR_R.N2Ind6
|}


  RNA samples prepared on lab note [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/SingleCell/2011-6-4]. Briefly, ES (~50cells) samples from Dr. Yi Zhang lab were directly lysated (named EL sample) or purified with RNA by Zymo kit (named ER sample), and then amplified with PCR_based protocol, which introduces poly(dT) to 5' end and poly(dA) to 3' end of the ds cDNA. Solexa Y adaptor was ligated to the ends and illumina barcoded primers (N2.ID12 and N2.ID13) were used to amplfied EL and ER samples, respectively.
  Sample description: [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:Collaborations]
Methods:
GFP+ and GFP-: [http://genome-tech.ucsd.edu/LabNotes/index.php/Kun:LabNotes/SingleCellExpr/2011-7-5#PCR_products]
E9.5 to E13.5f: [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-7-6]
Shearing: [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-7-8#Covaris_shearing_DNAs]
RNA library: [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-7-11]
Final check: [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Collaborations/2011-7-12]


Finally, Hap samples and RNA samples were mixed as 10:1:1 ratio for sequencing.
6.8.11: '''RL-Hap_RNAseq-1_13-Jun6'''


==Manuals==
{| {{table}} border=1
===Sequencing for Genewiz===
| align="center" style="background:#f0f0f0;"|'''Sample ID'''
Prepare for sequencing (Genewiz): 20ng DNA in 10ul total volume + 5ul 5uM primer
| align="center" style="background:#f0f0f0;"|'''Source'''
| align="center" style="background:#f0f0f0;"|'''Genome'''
| align="center" style="background:#f0f0f0;"|'''IndX'''
|-
| Hap1||GM12878||human||Nextera ID1
|-
| Hap2||GM12878||human||Nextera ID2
|-
| Hap3||GM12878||human||Nextera ID3
|-
| Hap4||GM12878||human||Nextera ID4
|-
| Hap5||GM12878||human||Nextera ID5
|-
| Hap6||GM12878||human||Nextera ID6
|-
| Hap7||GM12878||human||Nextera ID7
|-
| Hap8||GM12878||human||Nextera ID8
|-
| Hap9||GM12878||human||Nextera ID9
|-
| Hap10||GM12878||human||Nextera ID10
|-
| Hap11||GM12878||human||Nextera ID11
|-
| Hap12||GM12878||human||Nextera ID12
|-
| RNA-EL||Mm ES (50 cells)||mouse||PCR_R.N2Ind12
|-
| RNA-ER||Mm ES (50 cells)||mouse||PCR_R.N2Ind13
|}


===Zeroblunt cloning===
*Vector map [[File:zeroblunt vector map.pdf]]
*zeroblunt-topo Manual [[File:zerobluntTOPO man.pdf]]
*zeroblunt manual [[File:zeroblunt man.pdf]]


===TA cloning===
Hap samples (1-12) prepared on lab note 6.6.11 [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/Haplotyping/2011-6-6#2nd_round_of_PCR]. Briefly, Twelve cell lysate aliquots (~1pg gDNA) were amplified with Nextera adapter mix (barcode 1-12) and mixed the 12 samples at 1:1 ratio.
Vector map [http://products.invitrogen.com/ivgn/product/KNM204001]


Manual [[File:Original TA cloning kit.pdf]]
RNA samples prepared on lab note [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/SingleCell/2011-6-4]. Briefly, ES (~50cells) samples from Dr. Yi Zhang lab were directly lysated (named EL sample) or purified with RNA by Zymo kit (named ER sample), and then amplified with PCR_based protocol, which introduces poly(dT) to 5' end and poly(dA) to 3' end of the ds cDNA. Solexa Y adaptor was ligated to the ends and illumina barcoded primers (N2.ID12 and N2.ID13) were used to amplfied EL and ER samples, respectively.


===Bio-Rad QPCR machine===
Finally, Hap samples and RNA samples were mixed as 10:1:1 ratio for sequencing.
#Program on desktop: "Opticon Moniter 3"
#Instrument: Chromo4:CD003042. "Instrument"-->"Scan for instruments" or "Quick load"(under "Master")-->choose "Chromo4:CD003042"
#"Prepare new run" or "open" a old file and "edit"
#"Plate setup"-->"edit"-->select "samples" and "SBG1" for SYBR green I
#"Protocol setup"-->"edit"-->add "plate read" before "repeat cycle"
#"Melting curve" optional, hold at 15C, volume 20ul
#"Run" and "Save", files are saved in "Opticon Users 3"/Rui
#"Status" and "Quantitation" are used for monitoring PCR process
#"Quantitation"-->"copy to clipboard"-->"Data graph" and edit under "Paint"


===Ep Realplex QPCR machine===
==Buffer, material and manual==
#"Mastercycler ep realplex" on desktop
*[[Rui:Common buffers|Common buffers]]
#log in User name: "EPPENDORF", password: "e"
*[[Rui:Cell aliquot|Cell aliquot]]
#"PCR program"-->direct change temp and time-->right click to insert and advance edit
*[[Rui:Classic Illumina library process|Classic Illumina library process]]
#"Plate layout"-->"Filer 520nm"-->"SYBR"; "Sample volume", "Probe"-->"SYBR green", "Background"-->"Biorad strip tube-50ul" (Attention!); select sample area--> right click-->"unknown"-->ID
*[[Rui:SMARTer_clontech|SMARTer_clontech]]
#"Save as" a "template" or an "assay"
*[[Rui:Nextera-illumina|Nextera-illumina]]
#"Set up"-->"System Configuration"-->"Cycler"-->"Lid"-->select "Heat"-->Okey and close for preheat the lid
*[[Rui:Sequencing for Genewiz|Sequencing for Genewiz]]
#"Monitoring" for PCR process
*[[Rui:Zeroblunt cloning|Zeroblunt cloning]]
#"Analysis data" and save as assay
*[[Rui:TA cloning|TA cloning]]
*[[Rui:Bio-Rad QPCR machine|Bio-Rad QPCR machine]]
*[[Rui:Ep Realplex QPCR machine|Ep Realplex QPCR machine]]
*[[Rui:Microscope|Microscope]]
*[[Rui:Microincubator|Microincubator]]


===Microscope===
==Handy tools for wiki==
* Add colors to wiki[http://meta.wikimedia.org/wiki/Wiki_color_formatting_help]

Latest revision as of 01:59, 18 September 2014


Sample record for sequencing[edit]

colonyD and F samples for Hiseq[edit]

RL-D2.P0_24-May15; RL-D3.P0_24-May15

D_p0:[1] [2]

RL-N/A-D/F_p5-Jun6

D/F_p5:[3]

5.16.12 samples for Hiseq[edit]

RL-KH-Tn5mC-May16

' Label (cells) Cell # Label (Tn5mCseq) Primer Indx Label (pool) Seq Run
KH_Tn5mC_73 Female/Wt/Somatic(1) 4,342 KH_1_5.15.12 Nx Indx73 RL-KH-Tn5mC-May16 Hiseq_Apr25
KH_Tn5mC_74 Female/Wt/Somatic(2) 3,906 KH_2_5.15.12 Indx74 6 lanes
KH_Tn5mC_75 Female/Wt/PGC(1) 3,728 KH_3_5.15.12 Indx75
KH_Tn5mC_77 Female/homo/Somatic(1) 4,291 KH_5_5.15.12 Indx77
KH_Tn5mC_78 Female/homo/Somatic(2) 4,254 KH_6_5.15.12 Indx78
KH_Tn5mC_79 Female/homo/PGC(1) 3,266 KH_7_5.15.12 Indx79
KH_Tn5mC_80 Female/homo/PGC(2) 4,700 KH_8_5.15.12 Indx80
A3_Tn5mC_86 dFib_iPSC_A3p0 unknown An_A3_5.15.12 Nx Indx86
KH_Tn5mC_76 Female/Wt/PGC(2) 1,575 KH_4_5.15.12 Indx76 HL119

5.2.12 samples for Hiseq[edit]

' Template DNA Prmier Index Label in strip Label (pool)
D-p15_Indx73 D-p15 5ng Nextera Indx73 D1 RL_dFB_D-p15_24_5.2.12
D-p15_Indx74 5ng/ul Indx74 D1
D-p15_Indx75 Indx75 D1
D-p15_Indx76 Indx76 D1
D-p15_Indx77 Indx77 D1
D-p15_Indx78 Indx78 D1
D-p15_Indx79 Indx79 D1
D-p15_Indx80 Indx80 D1
D-p15_Indx81 Indx81 D2
D-p15_Indx82 Indx82 D2
D-p15_Indx83 Indx83 D2
D-p15_Indx84 Indx84 D2
D-p15_Indx85 Indx85 D2
D-p15_Indx86 Indx86 D2
D-p15_Indx87 Indx87 D2
D-p15_Indx88 Indx88 D2
D-p15_Indx89 Indx89 D3
D-p15_Indx90 Indx90 D3
D-p15_Indx91 Indx91 D3
D-p15_Indx92 Indx92 D3
D-p15_Indx93 Indx93 D3
D-p15_Indx94 Indx94 D3
D-p15_Indx95 Indx95 D3
D-p15_Indx96 Indx96 D3
' Template DNA Prmier Index Label in strip Label (pool)
F-p15_Indx73 F-p15 5ng Nextera Indx73 F1 RL_dFB_F-p15_24_5.2.12
F-p15_Indx74 5ng/ul Indx74 F1
F-p15_Indx75 Indx75 F1
F-p15_Indx76 Indx76 F1
F-p15_Indx77 Indx77 F1
F-p15_Indx78 Indx78 F1
F-p15_Indx79 Indx79 F1
F-p15_Indx80 Indx80 F1
F-p15_Indx81 Indx81 F2
F-p15_Indx82 Indx82 F2
F-p15_Indx83 Indx83 F2
F-p15_Indx84 Indx84 F2
F-p15_Indx85 Indx85 F2
F-p15_Indx86 Indx86 F2
F-p15_Indx87 Indx87 F2
F-p15_Indx88 Indx88 F2
F-p15_Indx89 Indx89 F3
F-p15_Indx90 Indx90 F3
F-p15_Indx91 Indx91 F3
F-p15_Indx92 Indx92 F3
F-p15_Indx93 Indx93 F3
F-p15_Indx94 Indx94 F3
F-p15_Indx95 Indx95 F3
F-p15_Indx96 Indx96 F3


4.24.12 samples for HL118/Hiseq[edit]

' Label (cells) Cell # Label (RNAseq) Primer Indx Label (pool) Seq Run
ES1 H9/45 ES, 11/4/11 1000 wei#1_4.9.12 illumina N2 Indx73 RL_wei1-12_4.10.12 Hiseq_
ES2 H9/50 ES, 11/28 1000 wei#2_4.9.12 Indx74 1 lane
DE1 H9/41 DE, 10/20 1000 wei#3_4.9.12 Indx75
DE2 H9/46f DE, 10/31 1000 wei#4_4.9.12 Indx76
PP1 S3/f, 10/14 1000 wei#5_4.9.12 Indx77
PP2 S3/f P2, 10/14 1000 wei#6_4.9.12 Indx78
PP3 62M, 24+, 10/26 1000 wei#7_4.9.12 Indx79
a1 alpha, 11/17 1000 wei#8_4.9.12 Indx80
a2 alpha, 11/11 1000 wei#9_4.9.12 Indx81
b1 beta, 11/17 1000 wei#10_4.9.12 Indx82
b2 beta, 11/11 1000 wei#11_4.9.12 Indx83
Px Px+, 11/17 1000 wei#12_4.9.12 Indx84
' Label (strip) re-mix (ul) primer Indx Label (pool) Seq Run
B2_Indx73 B2_1A 1.49 Nextera Indx73 RL_4.24.12_B2(remix)-23 HiSeq_
B2_Indx74 B2_1B 2.25 Indx74 2 lanes
B2_Indx75 B2_1C 0.98 Indx75
B2_Indx76 B2_1D 1.08 Indx76
B2_Indx77 B2_1E 1.34 Indx77
B2_Indx78 B2_1F 1.11 Indx78
B2_Indx79 B2_1G 1.06 Indx79
B2_Indx80 B2_1H 1.61 Indx80
B2_Indx81 B2_2A 1.41 Indx81
B2_Indx82 B2_2B 1.15 Indx82
B2_Indx83 B2_2C 1.05 Indx83
B2_Indx84 B2_2D 0.92 Indx84
B2_Indx85 B2_2E 1.60 Indx85
B2_Indx86 B2_2F 1.09 Indx86
B2_Indx87 B2_2G 2.08 Indx87
B2_Indx88 B2_2H 1.69 Indx88
B2_Indx89 B2_3A 10.00 Indx89
B2_Indx90 B2_3B 1.07 Indx90
B2_Indx91 B2_3C 0.88 Indx91
B2_Indx92 B2_3D 1.36 Indx92
B2_Indx93 B2_3E 3.00 Indx93
B2_Indx94 B2_3F 1.80 Indx94
B2_Indx95 B2_3G 1.23 Indx95
B3_Indx73 B3_1A 3 Nextera Indx73 RL_4.24.12_B3(remix)-23 HiSeq_
B3_Indx74 B3_1B 1.49 Indx74 2 lanes
B3_Indx75 B3_1C 0.86 Indx75
B3_Indx76 B3_1D 1.52 Indx76
B3_Indx77 B3_1E 1.66 Indx77
B3_Indx78 B3_1F 1.72 Indx78
B3_Indx79 B3_1G 2.04 Indx79
B3_Indx80 B3_1H 1.95 Indx80
B3_Indx81 B3_2A 1.48 Indx81
B3_Indx82 B3_2B 1.28 Indx82
B3_Indx83 B3_2C 1.31 Indx83
B3_Indx84 B3_2D 1.78 Indx84
B3_Indx85 B3_2E 1.82 Indx85
B3_Indx86 B3_2F 1.51 Indx86
B3_Indx87 B3_2G 1.17 Indx87
B3_Indx88 B3_2H 1.01 Indx88
B3_Indx90 B3_3B 1.57 Indx90
B3_Indx91 B3_3C 2.35 Indx91
B3_Indx92 B3_3D 1.94 Indx92
B3_Indx93 B3_3E 1.22 Indx93
B3_Indx94 B3_3F 1.66 Indx94
B3_Indx95 B3_3G 1.14 Indx95
B3_Indx96 B3_3H 1.43 Indx96
' Label (cells) DNA Prmier Index Label in strip Nextera Indx Label (pool)
Fib_Indx73 Fib_bulk 6ng Nextera Indx73 F1 RL_4.24.12_FIB-24 HiSeq_
Fib_Indx74 6ng/ul Indx74 F1 1 lanes
Fib_Indx75 Indx75 F1
Fib_Indx76 Indx76 F1
Fib_Indx77 Indx77 F1
Fib_Indx78 Indx78 F1
Fib_Indx79 Indx79 F1
Fib_Indx80 Indx80 F1
Fib_Indx81 Indx81 F2
Fib_Indx82 Indx82 F2
Fib_Indx83 Indx83 F2
Fib_Indx84 Indx84 F2
Fib_Indx85 Indx85 F2
Fib_Indx86 Indx86 F2
Fib_Indx87 Indx87 F2
Fib_Indx88 Indx88 F2
Fib_Indx89 Indx89 F3
Fib_Indx90 Indx90 F3
Fib_Indx91 Indx91 F3
Fib_Indx92 Indx92 F3
Fib_Indx93 Indx93 F3
Fib_Indx94 Indx94 F3
Fib_Indx95 Indx95 F3
Fib_Indx96 Indx96 F3
B-P30_Indx73 dFB_B_P30 5ng Nextera Indx73 P30-1 RL_4.24.12_B-P30-24 HiSeq_
B-P30_Indx74 5ng/ul Indx74 P30-1 2 lanes
B-P30_Indx75 Indx75 P30-1
B-P30_Indx76 Indx76 P30-1
B-P30_Indx77 Indx77 P30-1
B-P30_Indx78 Indx78 P30-1
B-P30_Indx79 Indx79 P30-1
B-P30_Indx80 Indx80 P30-1
B-P30_Indx81 Indx81 P30-2
B-P30_Indx82 Indx82 P30-2
B-P30_Indx83 Indx83 P30-2
B-P30_Indx84 Indx84 P30-2
B-P30_Indx85 Indx85 P30-2
B-P30_Indx86 Indx86 P30-2
B-P30_Indx87 Indx87 P30-2
B-P30_Indx88 Indx88 P30-2
B-P30_Indx89 Indx89 P30-3
B-P30_Indx90 Indx90 P30-3
B-P30_Indx91 Indx91 P30-3
B-P30_Indx92 Indx92 P30-3
B-P30_Indx93 Indx93 P30-3
B-P30_Indx94 Indx94 P30-3
B-P30_Indx95 Indx95 P30-3
B-P30_Indx96 Indx96 P30-3

3.8.12 sample for HiSeq_120313[edit]

RL_B2_23s_Mar8.2012
Sample ID Index Adapter
B2-1 Indx73 Nextera
B2-2 Indx74 Nextera
B2-3 Indx75 Nextera
B2-4 Indx76 Nextera
B2-5 Indx77 Nextera
B2-6 Indx78 Nextera
B2-7 Indx79 Nextera
B2-8 Indx80 Nextera
B2-9 Indx81 Nextera
B2-10 Indx82 Nextera
B2-11 Indx83 Nextera
B2-12 Indx84 Nextera
B2-13 Indx85 Nextera
B2-14 Indx86 Nextera
B2-15 Indx87 Nextera
B2-16 Indx88 Nextera
B2-17 Indx89 Nextera
B2-18 Indx90 Nextera
B2-19 Indx91 Nextera
B2-20 Indx92 Nextera
B2-21 Indx93 Nextera
B2-22 Indx94 Nextera
B2-23 Indx95 Nextera
RL_B3_24s_Mar8.2012
Sample ID Index Adapter
B3-1 Indx73 Nextera
B3-2 Indx74 Nextera
B3-3 Indx75 Nextera
B3-4 Indx76 Nextera
B3-5 Indx77 Nextera
B3-6 Indx78 Nextera
B3-7 Indx79 Nextera
B3-8 Indx80 Nextera
B3-9 Indx81 Nextera
B3-10 Indx82 Nextera
B3-11 Indx83 Nextera
B3-12 Indx84 Nextera
B3-13 Indx85 Nextera
B3-14 Indx86 Nextera
B3-15 Indx87 Nextera
B3-16 Indx88 Nextera
B3-17 Indx89 Nextera
B3-18 Indx90 Nextera
B3-19 Indx91 Nextera
B3-20 Indx92 Nextera
B3-21 Indx93 Nextera
B3-22 Indx94 Nextera
B3-23 Indx95 Nextera
B3-24 Indx96 Nextera
RL_Fib-Bulk_Mar8.2012: Indx96, Nextera


Lab note: B2 [4] B3 [5] Fib-bulk [6]

Final gel check: 1, 3, 4 lanes in this link [7]

1.31.12 sample for HL114[edit]

RL_Fib100c_29s_ExoCap_Jan31.2012 (L2, L3)

Lab note: [8] [9]

ID Sample MDA Index
U-1 Human MM Indx73
U-2 Fibroblast MM Indx74
U-3 100c MM Indx75
U-4 MM Indx76
U-5 ~5c/well MM Indx77
U-6 MDA 1.5hrs MM Indx78
U-7 MM Indx79
U-8 Tn-I PCR MM Indx80
U-9 MM Indx81
U-10 900ng for MM Indx82
U-11 ExoCap MM Indx83
U-12 MM Indx84
U-13 MM Indx85
U-14 MM Indx86
U-15 MM Indx87
U-16 MM Indx88
A1-2 Aliquot-cool Indx90
A1-3 Aliquot-cool Indx91
A1-4 Aliquot-cool Indx92
A1-5 Aliquot-cool Indx93
A1-6 Aliquot-cool Indx94
A1-7 Aliquot-cool Indx95
A1-8 Aliquot-cool Indx96
A2-3 Aliquot-RT Indx3
A2-4 Aliquot-RT Indx4
A2-5 Aliquot-RT Indx5
A2-6 Aliquot-RT Indx6
A2-7 Aliquot-RT Indx7
A2-8 Aliquot-RT Indx8
RL_EF_ExoCap_Jan31.2012 (L7)

Lab note: [10] [11]

ID Sample Method Index
ES hES Tn-I PCR Indx1
Fib hFibroblast ExoCap Indx2

HL113 and HiSeqFeb09[edit]

HiSeqFeb09: ru-mix samples based on read ratio in HL113, HiSeqFeb09 L1-3

Lab note: [12]

RL_BAC_73-96_12.22.11
A1 Indx73 Nextera
B1 Indx74 Nextera
C1 Indx75 Nextera
D1 Indx76 Nextera
E1 Indx77 Nextera
F1 Indx78 Nextera
G1 Indx79 Nextera
A2 Indx81 Nextera
B2 Indx82 Nextera
C2 Indx83 Nextera
D2 Indx84 Nextera
E2 Indx85 Nextera
F2 Indx86 Nextera
G2 Indx87 Nextera
H2 Indx88 Nextera
B3 Indx90 Nextera
C3 Indx91 Nextera
D3 Indx92 Nextera
E3 Indx93 Nextera
F3 Indx94 Nextera
G3 Indx95 Nextera
H3 Indx96 Nextera

HL108[edit]

  • Haplotyping samples from new protocol - MDA followed by Nextera
  • Lab note on 11.3.11 and 11.4.11 [13][14]
  • Finally hap library including Indx73-80
RL-Hap-73_80-Nov8 [RL_hap_Indx73-80_11.8.11 in tube label]
Sample ID Source Genome IndX
Hap1 GM12878-p15, MDA 17ct-2 human GA-Indx73
Hap2 GM12878-p15, MDA 22ct-3 GA-Indx74
Hap3 GM12878-p15, MDA 27ct-3 GA-Indx75
Hap4 GM12878-p15, MDA 27ct-4 GA-Indx76
Hap5 GM12878-p15, MDA 30ct-1 GA-Indx77
Hap6 GM12878-p15, MDA 30ct-2 GA-Indx78
Hap7 GM12878-p15, MDA 30ct-3 GA-Indx79
Hap8 GM12878-p15, MDA 30ct-4 GA-Indx80

HL106/HL109[edit]

  • RNA libraries for Dr. Yi Zhang and Dr. Xu Yang lab
  • The library probably has over-amplified issue, which may have more clonal reads [15]
  • Complete notes for RNAseq libraries are from 10.3.11-10.8.11 (cDNA) and 10.11.11-10.13.11 (libraries)
  • Final gel check [16]
RL_RNAseq_Indx88-96_10.18.11
Sample Source Genome Index '
Ctrl-0d Yi Zhang Human PCR_R.N2.Indx88
B1-0d Yi Zhang Human PCR_R.N2.Indx89
B3-0d Yi Zhang Human PCR_R.N2.Indx90
Ctrl-2d Yi Zhang Human PCR_R.N2.Indx91
B1-2d Yi Zhang Human PCR_R.N2.Indx92
B3-2d Yi Zhang Human PCR_R.N2.Indx93
Ctrl Xu Yang Human PCR_R.N2.Indx94
RFP Xu Yang Human PCR_R.N2.Indx95
GFP+RFP Xu Yang Human PCR_R.N2.Indx96

HL101[edit]

Haplotyping samples[edit]

  1. Lyse the cell aliquot #1 (10 cells) in 60 lysis buffer, aliquot 1ul cell lysates to 24 tubes and process with Nextera haplotyping protocol. Barcode the first 12 cell lysates with Nextera 1-12 as RL_hap1-12; barcode the second 12 cell lysates with Nextera 1-12 as RL_12-23 (w/o lysate #21). Individual hap samples were made on 8.23.11 [17] and size selection of pooled samples were made by Matt
  2. Lyse the cell aliquot #2 (10 cells) in 60 lysis buffer, aliquot 1ul cell lysates to 12 tubes and process with Nextera haplotyping protocol. Barcode the 12 cell lysates with Nextera 1-12 as MC_hap1-11 (w/o lysate #6). Individual hap samples were made by Matt on 8.24.11 [18] and size selection of pooled samples were made by Matt
  3. Final check on 9.2.11 lab note [19]
RL_hap1-12_9.2.11
Sample ID Source Genome IndX
Hap1 GM12878-p15, cell aliquot #1, lysate #1 human Nextera ID1
Hap2 GM12878-p15, cell aliquot #1, lysate #2 Nextera ID2
Hap3 GM12878-p15, cell aliquot #1, lysate #3 Nextera ID3
Hap4 GM12878-p15, cell aliquot #1, lysate #4 Nextera ID4
Hap5 GM12878-p15, cell aliquot #1, lysate #5 Nextera ID5
Hap6 GM12878-p15, cell aliquot #1, lysate #6 Nextera ID6
Hap7 GM12878-p15, cell aliquot #1, lysate #7 Nextera ID7
Hap8 GM12878-p15, cell aliquot #1, lysate #8 Nextera ID8
Hap9 GM12878-p15, cell aliquot #1, lysate #9 Nextera ID9
Hap10 GM12878-p15, cell aliquot #1, lysate #10 Nextera ID10
Hap11 GM12878-p15, cell aliquot #1, lysate #11 Nextera ID11
Hap12 GM12878-p15, cell aliquot #1, lysate #12 Nextera ID12
RL_hap13-23_9.2.11
Sample ID Source Genome IndX
Hap13 GM12878-p15, cell aliquot #1, lysate #13 human Nextera ID1
Hap14 GM12878-p15, cell aliquot #1, lysate #14 Nextera ID2
Hap15 GM12878-p15, cell aliquot #1, lysate #15 Nextera ID3
Hap16 GM12878-p15, cell aliquot #1, lysate #16 Nextera ID4
Hap17 GM12878-p15, cell aliquot #1, lysate #17 Nextera ID5
Hap18 GM12878-p15, cell aliquot #1, lysate #18 Nextera ID6
Hap19 GM12878-p15, cell aliquot #1, lysate #19 Nextera ID7
Hap20 GM12878-p15, cell aliquot #1, lysate #20 Nextera ID8
Hap21 GM12878-p15, cell aliquot #1, lysate #22 Nextera ID10
Hap22 GM12878-p15, cell aliquot #1, lysate #23 Nextera ID11
Hap23 GM12878-p15, cell aliquot #1, lysate #24 Nextera ID12
MC_hap1-11_9.2.11
Sample ID Source Genome IndX
Hap1 GM12878-p15, cell aliquot #2, lysate #1 human Nextera ID1
Hap2 GM12878-p15, cell aliquot #2, lysate #2 Nextera ID2
Hap3 GM12878-p15, cell aliquot #2, lysate #3 Nextera ID3
Hap4 GM12878-p15, cell aliquot #2, lysate #4 Nextera ID4
Hap5 GM12878-p15, cell aliquot #2, lysate #5 Nextera ID5
Hap6 GM12878-p15, cell aliquot #2, lysate #7 Nextera ID7
Hap7 GM12878-p15, cell aliquot #2, lysate #8 Nextera ID8
Hap8 GM12878-p15, cell aliquot #2, lysate #9 Nextera ID9
Hap9 GM12878-p15, cell aliquot #2, lysate #10 Nextera ID10
Hap10 GM12878-p15, cell aliquot #2, lysate #11 Nextera ID11
Hap11 GM12878-p15, cell aliquot #2, lysate #12 Nextera ID12

RNA libraries for Dr. Yi Zhang lab[edit]

  1. E9.5 (Indx3), E11.5 (Indx4), E13.5m1 (Indx5), and E13.5f1 (Indx6) are from amplified RNAs on lab note 7.11.11 [20] and re-amplify with the rest of N2 adapter-ligated products on 9.1.11 [21]
  2. E9.5 (Indx7), E11.5 (Indx8), KO E13.5m (Indx13), KO E13.5f1 (Indx14), and KO E13.5f2 (Indx15) samples are from amplified RNAs on lab note 8.30.11 [22]
  3. E13.5m1 (Indx9), E13.5m2 (Indx10), E13.5f1 (Indx11), and E13.5f2 (Indx12) are from amplified RNAs on lab note 8.31.11 [23]
  4. spike-in RNA amount = (total amount of each sample X 8) / 10,000 (based on Dr. Zhang's assumption) for samples in No.2 and No.3 on lab note 8.31.11 [24]
  5. Libraries processing is on lab note 8.31.11 and 9.1.11 [25][26]
  6. Final check in on lab note 9.2.11 [27]
RL_RNAIndx7-15_9.2.11
Sample Source Barcode
E9.5 Mouse PCR_R.N2Ind3
E11.5 PCR_R.N2Ind4
wt E13.5m1 PCR_R.N2Ind5
wt E13.5f1 PCR_R.N2Ind6
E9.5 + spike-in RNAs PCR_R.N2Ind7
E11.5 + spike-in RNAs PCR_R.N2Ind8
wt E13.5m1 + spike-in RNAs PCR_R.N2Ind9
wt E13.5m2 + spike-in RNAs PCR_R.N2Ind10
wt E13.5f1 + spike-in RNAs PCR_R.N2Ind11
wt E13.5f2 + spike-in RNAs PCR_R.N2Ind12
KO E13.5m + spike-in RNAs PCR_R.N2Ind13
KO E13.5f1 + spike-in RNAs PCR_R.N2Ind14
KO E13.5f2 + spike-in RNAs PCR_R.N2Ind15

HL099[edit]

7.25.11: RL-RNAseq-1_4-July25

Sample Original volume Mappable reads Modified volume IndX
GFP+ 2.55 0.8M 5.1 PCR_R.N2Ind1
GFP- 2 1.6M 2 PCR_R.N2Ind2
E9.5 3.04 1.5M 3.3 PCR_R.N2Ind3
E11.5 2.39 1.2M 3.18 PCR_R.N2Ind4


HL098[edit]

7.13.11: RL-RNAseq-1_6-July12

Sample ID Source Genome IndX
GFP+ Xu Yang lab human PCR_R.N2Ind1
GFP- Xu Yang lab human PCR_R.N2Ind2
E9.5 Yi Zhang lab mouse PCR_R.N2Ind3
E11.5 Yi Zhang lab mouse PCR_R.N2Ind4
E13.5m Yi Zhang lab mouse PCR_R.N2Ind5
E13.5f Yi Zhang lab mouse PCR_R.N2Ind6
Sample description: [28]

Methods: 
GFP+ and GFP-: [29]
E9.5 to E13.5f: [30]
Shearing: [31]
RNA library: [32]
Final check: [33]

6.8.11: RL-Hap_RNAseq-1_13-Jun6

Sample ID Source Genome IndX
Hap1 GM12878 human Nextera ID1
Hap2 GM12878 human Nextera ID2
Hap3 GM12878 human Nextera ID3
Hap4 GM12878 human Nextera ID4
Hap5 GM12878 human Nextera ID5
Hap6 GM12878 human Nextera ID6
Hap7 GM12878 human Nextera ID7
Hap8 GM12878 human Nextera ID8
Hap9 GM12878 human Nextera ID9
Hap10 GM12878 human Nextera ID10
Hap11 GM12878 human Nextera ID11
Hap12 GM12878 human Nextera ID12
RNA-EL Mm ES (50 cells) mouse PCR_R.N2Ind12
RNA-ER Mm ES (50 cells) mouse PCR_R.N2Ind13


Hap samples (1-12) prepared on lab note 6.6.11 [34]. Briefly, Twelve cell lysate aliquots (~1pg gDNA) were amplified with Nextera adapter mix (barcode 1-12) and mixed the 12 samples at 1:1 ratio.
RNA samples prepared on lab note [35]. Briefly, ES (~50cells) samples from Dr. Yi Zhang lab were directly lysated (named EL sample) or purified with RNA by Zymo kit (named ER sample), and then amplified with PCR_based protocol, which introduces poly(dT) to 5' end and poly(dA) to 3' end of the ds cDNA. Solexa Y adaptor was ligated to the ends and illumina barcoded primers (N2.ID12 and N2.ID13) were used to amplfied EL and ER samples, respectively.
Finally, Hap samples and RNA samples were mixed as 10:1:1 ratio for sequencing.

Buffer, material and manual[edit]

Handy tools for wiki[edit]

  • Add colors to wiki[36]