Rui Liu: Difference between revisions

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==Sample record for sequencing==
==Sample record for sequencing==
===4.24.12 samples for 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===
===3.8.12 sample for HiSeq_120313===
  '''RL_B2_23s_Mar8.2012'''
  '''RL_B2_23s_Mar8.2012'''

Revision as of 19:44, 24 April 2012

Lab Projects

Sample record for sequencing

4.24.12 samples for Hiseq

' 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

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 [1] B3 [2] Fib-bulk [3]

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

1.31.12 sample for HL114

RL_Fib100c_29s_ExoCap_Jan31.2012 (L2, L3)

Lab note: [5] [6]

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: [7] [8]

ID Sample Method 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: [9]

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

  • Haplotyping samples from new protocol - MDA followed by Nextera
  • Lab note on 11.3.11 and 11.4.11 [10][11]
  • 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

  • RNA libraries for Dr. Yi Zhang and Dr. Xu Yang lab
  • The library probably has over-amplified issue, which may have more clonal reads [12]
  • 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 [13]
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

Haplotyping samples

  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 [14] 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 [15] and size selection of pooled samples were made by Matt
  3. Final check on 9.2.11 lab note [16]
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

  1. E9.5 (Indx3), E11.5 (Indx4), E13.5m1 (Indx5), and E13.5f1 (Indx6) are from amplified RNAs on lab note 7.11.11 [17] and re-amplify with the rest of N2 adapter-ligated products on 9.1.11 [18]
  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 [19]
  3. E13.5m1 (Indx9), E13.5m2 (Indx10), E13.5f1 (Indx11), and E13.5f2 (Indx12) are from amplified RNAs on lab note 8.31.11 [20]
  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 [21]
  5. Libraries processing is on lab note 8.31.11 and 9.1.11 [22][23]
  6. Final check in on lab note 9.2.11 [24]
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

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

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: [25]

Methods: 
GFP+ and GFP-: [26]
E9.5 to E13.5f: [27]
Shearing: [28]
RNA library: [29]
Final check: [30]

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 [31]. 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 [32]. 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