|
| Status |
Public on Jun 06, 2017 |
| Title |
2i – N2B27_BL6_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
2i – N2B27_BL6_Rep2
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6/J
passages: 15
|
| Growth protocol |
Cell sample specific- culture parameters included in title
|
| Extracted molecule |
polyA RNA |
| 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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNA-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
|
| |
|
| 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 |
SAMN06887185 |
| SRA |
SRX2781577 |
