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 | ||
{| {{table}} border = 1 | {| {{table}} border = 1 | ||
| align="center" style=" | | align="center" style="background:#f0f0f0;"|'''Library Name''' | ||
| align="center" style="width: | | align="center" style="width:80px;background:#f0f0f0;"|'''Sample ID''' | ||
| align="center" style="width:60px;background:#f0f0f0;"|'''Index#''' | |||
| align="center" style="width:60px;background:#f0f0f0;"|'''Index #''' | | align="center" style="width:80px;background:#f0f0f0;"|'''Index Sequence''' | ||
| align="center" style="width:80px;background:#f0f0f0;"|''' | | align="center" style="background:#f0f0f0;"|'''Adaptor/primer system''' | ||
| align="center" style=" | | align="center" style="width:60px;background:#f0f0f0;"|'''Sequencing lane''' | ||
| align="center" style="width:60px;background:#f0f0f0;"|''' | |||
|- | |- | ||
| NP-SeqCap-pCancerSetB-Dec4|| | | NP-SeqCap-pCancerSetB-Dec4 TS#1||PCP-2||1||ATCACG||TruSeq||1 | ||
|- | |- | ||
| NP-SeqCap-pCancerSetB-Dec4|| | | NP-SeqCap-pCancerSetB-Dec4 TS#3||PCP-4||3||TTAGGC||TruSeq||1 | ||
|- | |- | ||
| NP-SeqCap-pCancerSetB-Dec4|| | | NP-SeqCap-pCancerSetB-Dec4 TS#8||PCP-9||8||ACTTGA||TruSeq||1 | ||
|- | |- | ||
| NP-SeqCap-pCancerSetB-Dec4|| | | NP-SeqCap-pCancerSetB-Dec4 TS#9||6P-1||9||GATCAG||TruSeq||1 | ||
|- | |- | ||
| NP-SeqCap-pCancerSetB-Dec4|| | | NP-SeqCap-pCancerSetB-Dec4 TS#10||6P-2||10||TAGCTT||TruSeq||1 | ||
|- | |- | ||
| NP-SeqCap-pCancerSetB-Dec4|| | | NP-SeqCap-pCancerSetB-Dec4 TS#11||6P-3||11||GGCTAC||TruSeq||1 | ||
|- | |- | ||
| NP-SeqCap-pCancerSetB-Dec4|| | | NP-SeqCap-pCancerSetB-Dec4 TS#20||7P-3||20||GTGGCC||TruSeq||1 | ||
|- | |- | ||
| NP-SeqCap-pCancerSetB-Dec4|| | | NP-SeqCap-pCancerSetB-Dec4 TS#21||7P-5||21||GTTTCG||TruSeq||1 | ||
|- | |- | ||
| NP-SeqCap-pCancerSetB-Dec4||6 | | NP-SeqCap-pCancerSetB-Dec4 TS#22||7P-6||22||CGTACG||TruSeq||1 | ||
|- | |- | ||
| NP-SeqCap-pCancerSetB-Dec4|| | | NP-SeqCap-pCancerSetB-Dec4 TS#23||7P-7||23||GAGTGG||TruSeq||1 | ||
|- | |- | ||
| NP-SeqCap-pCancerSetB-Dec4|| | | NP-SeqCap-pCancerSetB-Dec4 TS#25||7P-8||25||ACTGAT||TruSeq||1 | ||
|- | |- | ||
| NP-SeqCap-pCancerSetB- | | NP-SeqCap-pCancerSetB-Dec4 TS#27||7P-10||27||ATTCCT||TruSeq||1 | ||
|- | |- | ||
| NP-SeqCap-pCancerSetB- | | NP-SeqCap-pCancerSetB-Dec4 TS#7||NC-7||7||CAGATC||TruSeq||1 | ||
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|- | |- | ||
| NP-SeqCap-tCancerSetC-Dec4 N2|| 6T-1||STD ILMN adaptor/PCR_R.N2 | | NP-SeqCap-tCancerSetC-Dec4 N2#20||6T-1||4||TGACCA||STD ILMN adaptor/PCR_R.N2 IndX||2 | ||
|- | |- | ||
| NP-SeqCap-tCancerSetC-Dec4 N2|| 6T-2||STD ILMN adaptor/PCR_R.N2 | | NP-SeqCap-tCancerSetC-Dec4 N2#21||6T-2||5||ACAGTG||STD ILMN adaptor/PCR_R.N2 IndX||2 | ||
|- | |- | ||
| NP-SeqCap-tCancerSetC-Dec4 N2|| 6T-3||STD ILMN adaptor/PCR_R.N2 | | NP-SeqCap-tCancerSetC-Dec4 N2#22||6T-3||6||GCCAAT||STD ILMN adaptor/PCR_R.N2 IndX||2 | ||
|- | |- | ||
| NP-SeqCap-tCancerSetC-Dec4 N2|| 6T-4||STD ILMN adaptor/PCR_R.N2 | | NP-SeqCap-tCancerSetC-Dec4 N2#23||6T-4||7||CAGATC||STD ILMN adaptor/PCR_R.N2 IndX||2 | ||
|- | |- | ||
| NP-SeqCap-tCancerSetC-Dec4 N2|| 6T-5||STD ILMN adaptor/PCR_R.N2 | | NP-SeqCap-tCancerSetC-Dec4 N2#24||6T-5||8||ACTTGA||STD ILMN adaptor/PCR_R.N2 IndX||2 | ||
|- | |- | ||
| NP-SeqCap-tCancerSetC-Dec4 N2|| 7T-1||STD ILMN adaptor/PCR_R.N2 | | NP-SeqCap-tCancerSetC-Dec4 N2#25||7T-1||9||GATCAG||STD ILMN adaptor/PCR_R.N2 IndX||2 | ||
|- | |- | ||
| NP-SeqCap-tCancerSetC-Dec4 N2|| 7T-2||STD ILMN adaptor/PCR_R.N2 | | NP-SeqCap-tCancerSetC-Dec4 N2#26||7T-2||10||TAGCTT||STD ILMN adaptor/PCR_R.N2 IndX||2 | ||
|- | |- | ||
| NP-SeqCap-tCancerSetC-Dec4 N2|| 7T-4||STD ILMN adaptor/PCR_R.N2 | | NP-SeqCap-tCancerSetC-Dec4 N2#28||7T-4||12||CTTGTA||STD ILMN adaptor/PCR_R.N2 IndX||2 | ||
|- | |- | ||
| NP-SeqCap-tCancerSetC-Dec4 N2|| 7T-5||STD ILMN adaptor/PCR_R.N2 | | NP-SeqCap-tCancerSetC-Dec4 N2#29||7T-5||13||CCATGA||STD ILMN adaptor/PCR_R.N2 IndX||2 | ||
|- | |- | ||
| NP-SeqCap-tCancerSetC-Dec4 N2|| PCT-1||STD ILMN adaptor/PCR_R.N2 | | NP-SeqCap-tCancerSetC-Dec4 N2#30||PCT-1||14||AAGACA||STD ILMN adaptor/PCR_R.N2 IndX||2 | ||
|- | |- | ||
| NP-SeqCap-tCancerSetC-Dec4 N2|| PCT-2||STD ILMN adaptor/PCR_R.N2 | | NP-SeqCap-tCancerSetC-Dec4 N2#31||PCT-2||15||CTTCCT||STD ILMN adaptor/PCR_R.N2 IndX||2 | ||
|- | |- | ||
| NP-SeqCap-tCancerSetC-Dec4 N2|| PCT-4||STD ILMN adaptor/PCR_R.N2 | | NP-SeqCap-tCancerSetC-Dec4 N2#32||PCT-4||16||GGGGTT||STD ILMN adaptor/PCR_R.N2 IndX||2 | ||
|- | |- | ||
| NP-SeqCap-tCancerSetC-Dec4 N2|| PCT-6||STD ILMN adaptor/PCR_R.N2 | | NP-SeqCap-tCancerSetC-Dec4 N2#33||PCT-6||17||CTCATC||STD ILMN adaptor/PCR_R.N2 IndX||2 | ||
|- | |- | ||
| NP-SeqCap-tCancerSetC-Dec4 N2|| PCT-7||STD ILMN adaptor/PCR_R.N2 | | NP-SeqCap-tCancerSetC-Dec4 N2#34||PCT-7||18||AGTTCA||STD ILMN adaptor/PCR_R.N2 IndX||2 | ||
|- | |- | ||
| NP-SeqCap-tCancerSetC-Dec4 | | NP-SeqCap-tCancerSetC-Dec4 TS#6||NC-6||6||GCCAAT||TruSeq||2 | ||
|} | |} |
Latest revision as of 03:03, 6 January 2015
Summary of WGBS sequencing libraries captured by SeqCap Hybridization capture and their corresponding index[edit]
1) HiSeq Rapid run at IGM (141216_SN1001_0423)[edit]
- 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 Name | Sample ID | Index# | Index Sequence | Adaptor/primer system | Sequencing lane |
NP-SeqCap-pCancerSetB-Dec4 TS#1 | PCP-2 | 1 | ATCACG | TruSeq | 1 |
NP-SeqCap-pCancerSetB-Dec4 TS#3 | PCP-4 | 3 | TTAGGC | TruSeq | 1 |
NP-SeqCap-pCancerSetB-Dec4 TS#8 | PCP-9 | 8 | ACTTGA | TruSeq | 1 |
NP-SeqCap-pCancerSetB-Dec4 TS#9 | 6P-1 | 9 | GATCAG | TruSeq | 1 |
NP-SeqCap-pCancerSetB-Dec4 TS#10 | 6P-2 | 10 | TAGCTT | TruSeq | 1 |
NP-SeqCap-pCancerSetB-Dec4 TS#11 | 6P-3 | 11 | GGCTAC | TruSeq | 1 |
NP-SeqCap-pCancerSetB-Dec4 TS#20 | 7P-3 | 20 | GTGGCC | TruSeq | 1 |
NP-SeqCap-pCancerSetB-Dec4 TS#21 | 7P-5 | 21 | GTTTCG | TruSeq | 1 |
NP-SeqCap-pCancerSetB-Dec4 TS#22 | 7P-6 | 22 | CGTACG | TruSeq | 1 |
NP-SeqCap-pCancerSetB-Dec4 TS#23 | 7P-7 | 23 | GAGTGG | TruSeq | 1 |
NP-SeqCap-pCancerSetB-Dec4 TS#25 | 7P-8 | 25 | ACTGAT | TruSeq | 1 |
NP-SeqCap-pCancerSetB-Dec4 TS#27 | 7P-10 | 27 | ATTCCT | TruSeq | 1 |
NP-SeqCap-pCancerSetB-Dec4 TS#7 | NC-7 | 7 | CAGATC | TruSeq | 1 |
NP-SeqCap-tCancerSetC-Dec4 N2#20 | 6T-1 | 4 | TGACCA | STD ILMN adaptor/PCR_R.N2 IndX | 2 |
NP-SeqCap-tCancerSetC-Dec4 N2#21 | 6T-2 | 5 | ACAGTG | STD ILMN adaptor/PCR_R.N2 IndX | 2 |
NP-SeqCap-tCancerSetC-Dec4 N2#22 | 6T-3 | 6 | GCCAAT | STD ILMN adaptor/PCR_R.N2 IndX | 2 |
NP-SeqCap-tCancerSetC-Dec4 N2#23 | 6T-4 | 7 | CAGATC | STD ILMN adaptor/PCR_R.N2 IndX | 2 |
NP-SeqCap-tCancerSetC-Dec4 N2#24 | 6T-5 | 8 | ACTTGA | STD ILMN adaptor/PCR_R.N2 IndX | 2 |
NP-SeqCap-tCancerSetC-Dec4 N2#25 | 7T-1 | 9 | GATCAG | STD ILMN adaptor/PCR_R.N2 IndX | 2 |
NP-SeqCap-tCancerSetC-Dec4 N2#26 | 7T-2 | 10 | TAGCTT | STD ILMN adaptor/PCR_R.N2 IndX | 2 |
NP-SeqCap-tCancerSetC-Dec4 N2#28 | 7T-4 | 12 | CTTGTA | STD ILMN adaptor/PCR_R.N2 IndX | 2 |
NP-SeqCap-tCancerSetC-Dec4 N2#29 | 7T-5 | 13 | CCATGA | STD ILMN adaptor/PCR_R.N2 IndX | 2 |
NP-SeqCap-tCancerSetC-Dec4 N2#30 | PCT-1 | 14 | AAGACA | STD ILMN adaptor/PCR_R.N2 IndX | 2 |
NP-SeqCap-tCancerSetC-Dec4 N2#31 | PCT-2 | 15 | CTTCCT | STD ILMN adaptor/PCR_R.N2 IndX | 2 |
NP-SeqCap-tCancerSetC-Dec4 N2#32 | PCT-4 | 16 | GGGGTT | STD ILMN adaptor/PCR_R.N2 IndX | 2 |
NP-SeqCap-tCancerSetC-Dec4 N2#33 | PCT-6 | 17 | CTCATC | STD ILMN adaptor/PCR_R.N2 IndX | 2 |
NP-SeqCap-tCancerSetC-Dec4 N2#34 | PCT-7 | 18 | AGTTCA | STD ILMN adaptor/PCR_R.N2 IndX | 2 |
NP-SeqCap-tCancerSetC-Dec4 TS#6 | NC-6 | 6 | GCCAAT | TruSeq | 2 |