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Sample GSM1178724 Query DataSets for GSM1178724
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

Supplementary file Size Download File type/resource
GSM1178724_Input.bw 46.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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