Rui Liu: Difference between revisions

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==Sample record for sequencing==
==Sample record for sequencing==
===HL?===
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}} border1
| 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===
===HL108===
* Haplotyping samples from new protocol - MDA followed by Nextera
* Haplotyping samples from new protocol - MDA followed by Nextera

Revision as of 20:06, 22 December 2011

Lab Projects

Sample record for sequencing

HL?

Lab note: [1]

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 [2][3]
  • 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 [4]
  • 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 [5]
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 [6] 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 [7] and size selection of pooled samples were made by Matt
  3. Final check on 9.2.11 lab note [8]
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 [9] and re-amplify with the rest of N2 adapter-ligated products on 9.1.11 [10]
  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 [11]
  3. E13.5m1 (Indx9), E13.5m2 (Indx10), E13.5f1 (Indx11), and E13.5f2 (Indx12) are from amplified RNAs on lab note 8.31.11 [12]
  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 [13]
  5. Libraries processing is on lab note 8.31.11 and 9.1.11 [14][15]
  6. Final check in on lab note 9.2.11 [16]
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: [17]

Methods: 
GFP+ and GFP-: [18]
E9.5 to E13.5f: [19]
Shearing: [20]
RNA library: [21]
Final check: [22]

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 [23]. 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 [24]. 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