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===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 |} 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] 6.8.11: '''RL-Hap_RNAseq-1_13-Jun6''' {| {{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||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 [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. 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. Finally, Hap samples and RNA samples were mixed as 10:1:1 ratio for sequencing.
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