Noi/NOTES/2014-12-5: Difference between revisions
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>Noi (Created page with "= WGBS library prep and BSPP capture of cfDNA from Illumina = '''Back to calendar'''<br> === Aims === * To generate 10 WGBS libraries from ctDNA ...") |
>Noi mNo edit summary |
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* To capture WGBS libraries with MONOD v5 (LMS) probe set from Zhang's lab and CRC probe set from Illumina | * To capture WGBS libraries with MONOD v5 (LMS) probe set from Zhang's lab and CRC probe set from Illumina | ||
=== Sample info === | === Sample info === | ||
{| {{table}} class = wikitable | |||
| align="center" style="width:140px;background:#f0f0f0;"|'''Subject#''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Sample_ID''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Plasma volume (ul)''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Size (bp) by BA''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Total Yield (ng) by BA''' | |||
|- | |||
| KUCC BRCF 011921||10.A13.3||964||187||14 | |||
|- | |||
| KUCC BRCF 005881||9.B7.36||952||178||13.2 | |||
|- | |||
| KUCC BRCF 007388||9.C28.47||876||173||11.9 | |||
|- | |||
| KUCC BRCF 008966||9.I19.36||882||185||4.8 | |||
|- | |||
| KUCC BRCF 008282||9.G9.25||670||191||9 | |||
|- | |||
| KUCC BRCF 008116||9.F20.56||924||197||5.1 | |||
|- | |||
| KUCC BRCF 007855||9.H5.58||914||223||8.6 | |||
|- | |||
| KUCC BRCF 008472||9.H3.25||1,000||219||4.6 | |||
|- | |||
| KUCC BRCF 008527||9.H7.69||1,150||237||11.1 | |||
|- | |||
| KUCC BRCF 008794||9.I7.3||770||249||9.57 | |||
|} | |||
* Each sample has volume ~22ul | |||
* Each sample has different amount of DNA and we want to use up all DNA for WGBS library prep. To make it simple for qPCR monitoring after adaptor ligation and bisulfite conversion, I re-named the sample ID and run based on the input DNA from low to high. | |||
{| {{table}} class = wikitable | |||
| align="center" style="width:140px;background:#f0f0f0;"|'''Subject#''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Sample_ID''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Total Yield (ng)by BA''' | |||
| align="center" style="width:100px;background:#f0f0f0;"|'''Zhang lab ID''' | |||
|- | |||
| KUCC BRCF 008472||9.H3.25||4.6||KU_1 | |||
|- | |||
| KUCC BRCF 008966||9.I19.36||4.8||KU_2 | |||
|- | |||
| KUCC BRCF 008116||9.F20.56||5.1||KU_3 | |||
|- | |||
| KUCC BRCF 007855||9.H5.58||8.6||KU_4 | |||
|- | |||
| KUCC BRCF 008282||9.G9.25||9||KU_5 | |||
|- | |||
| KUCC BRCF 008794||9.I7.3||9.57||KU_6 | |||
|- | |||
| KUCC BRCF 008527||9.H7.69||11.1||KU_7 | |||
|- | |||
| KUCC BRCF 007388||9.C28.47||11.9||KU_8 | |||
|- | |||
| KUCC BRCF 005881||9.B7.36||13.2||KU_9 | |||
|- | |||
| KUCC BRCF 011921||10.A13.3||14||KU_10 | |||
|} |
Revision as of 10:19, 7 December 2014
WGBS library prep and BSPP capture of cfDNA from Illumina
Aims
- To generate 10 WGBS libraries from ctDNA of colorectal cancer (CRC) patients from Illumina (received from Kansas University)
- To capture WGBS libraries with MONOD v5 (LMS) probe set from Zhang's lab and CRC probe set from Illumina
Sample info
Subject# | Sample_ID | Plasma volume (ul) | Size (bp) by BA | Total Yield (ng) by BA |
KUCC BRCF 011921 | 10.A13.3 | 964 | 187 | 14 |
KUCC BRCF 005881 | 9.B7.36 | 952 | 178 | 13.2 |
KUCC BRCF 007388 | 9.C28.47 | 876 | 173 | 11.9 |
KUCC BRCF 008966 | 9.I19.36 | 882 | 185 | 4.8 |
KUCC BRCF 008282 | 9.G9.25 | 670 | 191 | 9 |
KUCC BRCF 008116 | 9.F20.56 | 924 | 197 | 5.1 |
KUCC BRCF 007855 | 9.H5.58 | 914 | 223 | 8.6 |
KUCC BRCF 008472 | 9.H3.25 | 1,000 | 219 | 4.6 |
KUCC BRCF 008527 | 9.H7.69 | 1,150 | 237 | 11.1 |
KUCC BRCF 008794 | 9.I7.3 | 770 | 249 | 9.57 |
- Each sample has volume ~22ul
- Each sample has different amount of DNA and we want to use up all DNA for WGBS library prep. To make it simple for qPCR monitoring after adaptor ligation and bisulfite conversion, I re-named the sample ID and run based on the input DNA from low to high.
Subject# | Sample_ID | Total Yield (ng)by BA | Zhang lab ID |
KUCC BRCF 008472 | 9.H3.25 | 4.6 | KU_1 |
KUCC BRCF 008966 | 9.I19.36 | 4.8 | KU_2 |
KUCC BRCF 008116 | 9.F20.56 | 5.1 | KU_3 |
KUCC BRCF 007855 | 9.H5.58 | 8.6 | KU_4 |
KUCC BRCF 008282 | 9.G9.25 | 9 | KU_5 |
KUCC BRCF 008794 | 9.I7.3 | 9.57 | KU_6 |
KUCC BRCF 008527 | 9.H7.69 | 11.1 | KU_7 |
KUCC BRCF 007388 | 9.C28.47 | 11.9 | KU_8 |
KUCC BRCF 005881 | 9.B7.36 | 13.2 | KU_9 |
KUCC BRCF 011921 | 10.A13.3 | 14 | KU_10 |