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Sample GSM1089088 Query DataSets for GSM1089088
Status Public on Feb 28, 2013
Title 2P-Seq actD 2h
Sample type SRA
 
Source name 3T3 cells
Organism Mus musculus
Characteristics cell type: 3T3 cells
treatment: 2P protocol and actD for 2hr
Treatment protocol Actinomycin D was added at a final concentration of 10 ug/ml and treated for the indicated number of hours
Extracted molecule total RNA
Extraction protocol 2P-Seq, barcoded
trizol, poly(A)-selected RNA
2P-Seq: partial digested with RNase T1, poly(A)-primed reverse transcription, circularization, PCR and sequencing from putative poly(A) tail
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Reads were aligned the mouse mm9 genome using Bowtie. 3P-Seq reads were used to annotate poly(A) sites. Reads within +/- 20 nt of these annotated poly(A) sites were combined when calculating read totals for 2P-Seq datasets.
Genome_build: mm9
Supplementary_files_format_and_content: tab separated file: poly(A) site annotations, reads, half-lives, translation rates per poly(A) site
 
Submission date Feb 26, 2013
Last update date May 15, 2019
Contact name Noah Spies
Organization name Stanford University
Department Pathology
Lab Arend Sidow
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL13112
Series (1)
GSE44698 Global analyses of how 3' UTR-isoform choice influences mRNA stability and translational efficiency
Relations
SRA SRX246087
BioSample SAMN01931912

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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