Rui Liu: Difference between revisions
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*[[Rui:Data Analysis|Data Analysis]] | *[[Rui:Data Analysis|Data Analysis]] | ||
*[[Rui:RNAseq|RNAseq]] | *[[Rui:RNAseq|RNAseq]] | ||
*[[Rui:DNAseq|DNAseq]] | |||
*[[Rui:Haplotying|Haplotying]] | *[[Rui:Haplotying|Haplotying]] | ||
Revision as of 00:54, 7 December 2011
Lab Projects
Sample record for sequencing
HL108
- Haplotyping samples from new protocol - MDA followed by Nextera
- Lab note on 11.3.11 and 11.4.11 [1][2]
- 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 [3]
- 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 [4]
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
- 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 [5] 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 [6] and size selection of pooled samples were made by Matt
- Final check on 9.2.11 lab note [7]
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
- E9.5 (Indx3), E11.5 (Indx4), E13.5m1 (Indx5), and E13.5f1 (Indx6) are from amplified RNAs on lab note 7.11.11 [8] and re-amplify with the rest of N2 adapter-ligated products on 9.1.11 [9]
- 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 [10]
- E13.5m1 (Indx9), E13.5m2 (Indx10), E13.5f1 (Indx11), and E13.5f2 (Indx12) are from amplified RNAs on lab note 8.31.11 [11]
- 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 [12]
- Libraries processing is on lab note 8.31.11 and 9.1.11 [13][14]
- Final check in on lab note 9.2.11 [15]
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: [16] Methods: GFP+ and GFP-: [17] E9.5 to E13.5f: [18] Shearing: [19] RNA library: [20] Final check: [21]
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 [22]. 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 [23]. 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.