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Sample GSM3084077 Query DataSets for GSM3084077
Status Public on Apr 07, 2018
Title mES untreated r1
Sample type SRA
 
Source name Embryonic stem cells
Organism Mus musculus
Characteristics cell type: V6.5
Growth protocol V6.5 (C57BL/6-129) murine ES cells were grown on 0.2% gelatinized tissue culture plates in 2i media, DMEM-F12, 0.5X B27 supplement, 0.5X N2 supplement , an extra 0.5mM L-glutamine , 0.1mM b-mercaptoethanol, 1% Penicillin Streptomycin , 0.5X nonessential amino acids , 1000 U/ml LIF , 1μM PD0325901 , and 3μM CHIR99021
Extracted molecule polyA RNA
Extraction protocol RNA was extracted with RNeasy mini kit (Qiagen 74104).
TruSeq Stranded RNA library prep kit (Illumina) was used for preparation of libraries, followed by single-end sequencing
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Sequencing reads were aligned to the mm9 revision of the mouse reference genome using Tophat with –no-novel-juncs and -G set to a list of known RefSeq transcripts downloaded 2/1/17.
Per-transcript expression was quantified as RPKMs using RPKM_count from the RSeQC package.
Genome_build: mm9
Supplementary_files_format_and_content: RPKM
 
Submission date Apr 06, 2018
Last update date Apr 08, 2018
Contact name Richard A Young
E-mail(s) young_computation@wi.mit.edu
Phone 617-258-5219
Organization name Whitehead Institute for Biomedical Research
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL17021
Series (2)
GSE112807 Coactivator condensation at super-enhancers links phase separation and gene control (RNA-Seq)
GSE112808 Coactivator condensation at super-enhancers links phase separation and gene control
Relations
BioSample SAMN08875374
SRA SRX3898507

Supplementary file Size Download File type/resource
GSM3084077_mES_Untreated_r1.rpkm.txt.gz 262.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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