|
| Status |
Public on Nov 30, 2013 |
| Title |
Input |
| Sample type |
SRA |
| |
|
| Source name |
J1_input
|
| Organism |
Mus musculus |
| Characteristics |
cell line: J1
cell type: embryonic stem cells
rip antibody: none
|
| Growth protocol |
mouse embryonic stem cells J1 was cultured in ESGRO medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA IP was performed using RNA IP kit from Millipore according to manufacturer's protocol
library was generated by use of RNA Truseq kit from Illumina
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Sample 1
|
| Data processing |
library strategy: RIP-seq
Basecalls were performed by MiSeq reporter software
Reads were aligned to index of RefSeq transcripts, derived from UCSC table browser 01/29/2013, using bowtie 0.12.8, employing parameters -v2 -m10 -k10 --best --strata
Transcript coordinates were translated to mm9 genomic coordinates, and duplicate alignments resulting from overlapping transcripts were removed using custom scripts
Read coverage tracks were generated using bedtools 2.16.2
Genome_build: mm9
Supplementary_files_format_and_content: bigWig, read coverage
|
| |
|
| Submission date |
Jul 01, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Li Wang |
| Organization name |
NIH
|
| Street address |
111 T.W. Alexander Dr
|
| City |
Durham |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL16417 |
| Series (2) |
| GSE48436 |
The THO complex regulates pluripotency gene mRNA export to control embryonic stem cell self-renewal and somatic cell reprogramming (RNA-IP) |
| GSE51534 |
The THO complex regulates pluripotency gene mRNA export to control embryonic stem cell self-renewal and somatic cell reprogramming |
|
| Relations |
| BioSample |
SAMN02221907 |
| SRA |
SRX316951 |
