Noi/NOTES/2014-12-25: Difference between revisions

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[[noi:DMR220k_LabNotes#2014| '''Back to calendar''']]
[[noi:DMR220k_LabNotes#2014| '''Back to calendar''']]
== 1) HiSeq Rapid run at IGM (141216_SN1001_0423) ==
== 1) HiSeq Rapid run at IGM (141216_SN1001_0423) ==
* Library type: WGBS libraries generated by KAPA Hyper Prep kit (all cancer plasma samples). NC samples were generated by original method but lacked T4 DNA Pol, T4 polynucleotide kinase.
* The WGBS libraries were captured by Nimblegen SeqCap LMS probe.
* PE 100+7
* PE 100+7
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Revision as of 00:08, 26 December 2014

Summary of WGBS sequencing libraries captured by SeqCap Hybridization capture and their corresponding index

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1) HiSeq Rapid run at IGM (141216_SN1001_0423)

  • Library type: WGBS libraries generated by KAPA Hyper Prep kit (all cancer plasma samples). NC samples were generated by original method but lacked T4 DNA Pol, T4 polynucleotide kinase.
  • The WGBS libraries were captured by Nimblegen SeqCap LMS probe.
  • PE 100+7
Library ID (for sequencing) Sample ID Adaptor System/primers Index # Seq (RC) Sequencing platform/at Lane #
NP-SeqCap-pCancerSetB-Dec4 PC-P_3 TruSeq 2 CGATGT Rapid run/IGM 1
NP-SeqCap-pCancerSetB-Dec4 PC-P_5 TruSeq 4 TGACCA Rapid run/IGM 1
NP-SeqCap-pCancerSetB-Dec4 PC-P_6 TruSeq 5 ACAGTG Rapid run/IGM 1
NP-SeqCap-pCancerSetB-Dec4 PC-P_7 TruSeq 6 GCCAAT Rapid run/IGM 1
NP-SeqCap-pCancerSetB-Dec4 PC-P_8 TruSeq 7 CAGATC Rapid run/IGM 1
NP-SeqCap-pCancerSetB-Dec4 6-P-4 TruSeq 12 CTTGTA Rapid run/IGM 1
NP-SeqCap-pCancerSetB-Dec4 6-P-5 TruSeq 13 AGTCAA Rapid run/IGM 1
NP-SeqCap-pCancerSetB-Dec4 6-P-8 TruSeq 14 AGTTCC Rapid run/IGM 1
NP-SeqCap-pCancerSetB-Dec4 6-P-9 TruSeq 15 ATGTCA Rapid run/IGM 1
NP-SeqCap-pCancerSetB-Dec4 6-P-10 TruSeq 16 CCGTCC Rapid run/IGM 1
NP-SeqCap-pCancerSetB-Dec4 7-P-1 TruSeq 18 GTCCGC Rapid run/IGM 1
NP-SeqCap-pCancerSetB-Dec15 7-P-2 TruSeq 19 GTGAAA Rapid run/IGM 1
NP-SeqCap-pCancerSetB-Dec16 NC-29 TruSeq 23 GAGTGG Rapid run/IGM 1


Library ID (for sequencing) Sample ID Adaptor System/primers Index # Seq (RC) Sequencing platform/at Lane #
NP-SeqCap-tCancerSetC-Dec4 N2 6T-1 STD ILMN adaptor/PCR_R.N2 Indx 4 TGACCA Rapid run/IGM 2
NP-SeqCap-tCancerSetC-Dec4 N2 6T-2 STD ILMN adaptor/PCR_R.N2 Indx 5 ACAGTG Rapid run/IGM 2
NP-SeqCap-tCancerSetC-Dec4 N2 6T-3 STD ILMN adaptor/PCR_R.N2 Indx 6 GCCAAT Rapid run/IGM 2
NP-SeqCap-tCancerSetC-Dec4 N2 6T-4 STD ILMN adaptor/PCR_R.N2 Indx 7 CAGATC Rapid run/IGM 2
NP-SeqCap-tCancerSetC-Dec4 N2 6T-5 STD ILMN adaptor/PCR_R.N2 Indx 8 ACTTGA Rapid run/IGM 2
NP-SeqCap-tCancerSetC-Dec4 N2 7T-1 STD ILMN adaptor/PCR_R.N2 Indx 9 GATCAG Rapid run/IGM 2
NP-SeqCap-tCancerSetC-Dec4 N2 7T-2 STD ILMN adaptor/PCR_R.N2 Indx 10 TAGCTT Rapid run/IGM 2
NP-SeqCap-tCancerSetC-Dec4 N2 7T-4 STD ILMN adaptor/PCR_R.N2 Indx 12 CTTGTA Rapid run/IGM 2
NP-SeqCap-tCancerSetC-Dec4 N2 7T-5 STD ILMN adaptor/PCR_R.N2 Indx 13 CCATGA Rapid run/IGM 2
NP-SeqCap-tCancerSetC-Dec4 N2 PCT-1 STD ILMN adaptor/PCR_R.N2 Indx 14 AAGACA Rapid run/IGM 2
NP-SeqCap-tCancerSetC-Dec4 N2 PCT-2 STD ILMN adaptor/PCR_R.N2 Indx 15 CTTCCT Rapid run/IGM 2
NP-SeqCap-tCancerSetC-Dec4 N2 PCT-4 STD ILMN adaptor/PCR_R.N2 Indx 16 GGGGTT Rapid run/IGM 2
NP-SeqCap-tCancerSetC-Dec4 N2 PCT-6 STD ILMN adaptor/PCR_R.N2 Indx 17 CTCATC Rapid run/IGM 2
NP-SeqCap-tCancerSetC-Dec4 N2 PCT-7 STD ILMN adaptor/PCR_R.N2 Indx 18 AGTTCA Rapid run/IGM 2
NP-SeqCap-tCancerSetC-Dec4 N2 NC-6 TruSeq 6 GCCAAT Rapid run/IGM 2