|
Status |
Public on Jun 06, 2017 |
Title |
2i/LIF – GMEM/10% KSR_129_MethylC-seq |
Sample type |
SRA |
|
|
Source name |
2i/LIF – GMEM/10% KSR_129
|
Organism |
Mus musculus |
Characteristics |
strain: 129X1/SvJ passages: 16
|
Growth protocol |
Cell sample specific- culture parameters included in title
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Total RNA was extracted using RNAeasy mini kit (Qiagen) with on-column Dnase step, and 1μg was used for polyA RNA library construction. Libraries were prepared according to Illumina TruSeq v2.0 protocols
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|
|
Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
MethylC-seq
|
Data processing |
Reads were filtered to remove all reads with a quality score of < Q20. Mapping was performed with Tophat 2.0.6 RPKMs were generated from the ucsc mm10 gtf Bisulfite mapping was performed with Bismark 0.7.12 CpG calls were extracted with Bismark methylation extractor Genome_build: mm10 Supplementary_files_format_and_content: text file with RPKM values or Bismark output
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|
|
Submission date |
May 03, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Charles Bradshaw |
Organization name |
University of Cambridge
|
Department |
Gurdon Institute
|
Street address |
Tennis Court Road
|
City |
Cambridge |
ZIP/Postal code |
CB2 1QN |
Country |
United Kingdom |
|
|
Platform ID |
GPL17021 |
Series (1) |
GSE98517 |
Activation of Lineage-Regulators and Transposable Elements Across a Pluripotent Spectrum |
|
Relations |
BioSample |
SAMN06887205 |
SRA |
SRX2781613 |