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GEO help: Mouse over screen elements for information. |
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Status |
Public on Apr 07, 2018 |
Title |
mES untreated r1 |
Sample type |
SRA |
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Source name |
Embryonic stem cells
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Organism |
Mus musculus |
Characteristics |
cell type: V6.5
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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
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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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
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Submission date |
Apr 06, 2018 |
Last update date |
Apr 08, 2018 |
Contact name |
Richard A Young |
E-mail(s) |
young_computation@wi.mit.edu
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Phone |
617-258-5219
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Organization name |
Whitehead Institute for Biomedical Research
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Lab |
Young Lab
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Street address |
9 Cambridge Center
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City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02142 |
Country |
USA |
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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 |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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