Noi/NOTES/2014-12-5: Difference between revisions

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(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
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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

Back to calendar

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