Alice:Whole Genome Bisulfite Sequencing Lab Notes
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WGBS of mouse SCNT and iPSC (collaborate with Yang Xu lab)[edit]
- The goal of this project is to examine the methylation pattern of mouse SCNT and iPSC against mESC using whole genome bisulfite sequencing, and to characterize epigenetic signatures that resulted from different stem cell reprogramming methods.
- detailed experimental procedures can be found here: [| Link]
sample ID | N2 Index used | cell type | progenitor line | progenitor/donor mouse strain |
2A4F1 | N2 index 1 | iPSC | N/A (used TB_B6MEF in exome study) | C57BL/6J |
2A4F33 | N2 index 2 | iPSC | N/A (used TB_B6MEF in exome study) | C57BL/6J |
miPS B3 | N2 index 4 | iPSC | ZN_B6MEF | C57BL/6J |
1E12P20 | N2 index 5 | iPSC | TB_B6MEF | C57BL/6J |
nt ES P7 C | N2 index 6 | SCNT | B6MEF P0-3 | C57BL/6J |
nt ES P8 B | N2 index 7 | SCNT | B6MEF P0-3 | C57BL/6J |
NB 3 | N2 index 9 | SCNT | B6-P1-1 | C57BL/6J |
SCNT B12 | N2 index 10 | SCNT | B6-P1-2 | C57BL/6J |
B6 ES | N2 index 11 | ES | - | C57BL/6J |
129 ES | N2 index 12 | ES | - | - |
Sequencing statistics[edit]
- Data Source
- The samples were sequenced in the following runs:
- Hiseq 130104_SN1001
- GAIIx 121226_HL140 (lane 1 only)
- The samples were sequenced in the following runs:
Sample ID | N2 Index | total reads | mapped reads | mapping rate | total # of CpG sites covered (coverage >=5) | mean coverage (sites with coverage >=5) | mean methylation level (sites with coverage >=5) |
2A4F1 | 1 | 375578848 | 283699999 | 76% | 17510624 | 12.5 | 0.76 |
2A4F33 | 2 | 360720634 | 253128940 | 70% | 16863956 | 11.3 | 0.74 |
mipsB3 | 4 | 342349949 | 211416203 | 62% | 15215962 | 9.8 | 0.71 |
1E12P20 | 5 | 328678606 | 227406985 | 69% | 15865114 | 10.6 | 0.73 |
nt ES P7C | 6 | 315952780 | 205976115 | 65% | 15025471 | 9.6 | 0.57 |
nt ES P8B | 7 | 461470678 | 333879642 | 72% | 17852991 | 12.1 | 0.61 |
NB3 | 9 | 297479356 | 205398733 | 69% | 14210572 | 9.3 | 0.79 |
SCNTB12 | 10 | 322193316 | 228779506 | 71% | 16016176 | 11.1 | 0.73 |
B6ES | 11 | 310311719 | 214278139 | 69% | 15464407 | 10.5 | 0.74 |
129ES | 12 | 271922039 | 163956125 | 60% | 7433945 | 7.7 | 0.64 |