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Sample GSM3351269 Query DataSets for GSM3351269
Status Public on Jun 25, 2020
Title DCP1A KO clone C17 (replicate 2) RNA-seq
Sample type SRA
 
Source name embryonic stem cells
Organism Mus musculus
Characteristics developmental stage: undifferentiated ES cells
Sex: female
strain: C57BL/6J x CAST/EiJ hybrid
genotype/variation: DCP1A KO
Growth protocol Mouse ES cells were grown on gelatin coated plates in 2i+LIF-containing medium
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol extraction, rRNA was depleted and RNA fragmented by heating in presence of Mg2+, CDNA 1st strand was produced using random primers
NEBNext Ultra Directional RNA Second Strand Synthesis Module (E7550S) was used as described with NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina (E6240L) for multiplexed library preparation
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description RNAseq-DCP1aKO1.c.bw
RNAseq-DCP1aKO1.w.bw
Data processing Adaptors were trimmed using cutadapt
Reads were aligned to mm9 genome using TopHat2 (Kim et al., 2013)
Mapped reads were further analyzed by Homer(ver 4.8) (Heinz et al., 2010) to generate a raw read count table
DESeq2 package (Love et al. 2014) was used for downstream RNA-seq analysis
Strand-specific coverage files (bigwig format) were generated by using uniquely mapped reads normalized by fragments per million
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for strand-specific (w:watson, c:crick strand) and fpm normalized
 
Submission date Aug 22, 2018
Last update date Jun 25, 2020
Contact name Eric Aeby
E-mail(s) aeby@molbio.mgh.harvard.edu
Organization name Howard Hughes Medical Institute, Massachusetts General HospitalMassachusetts General Hospital, Harvard Medical School
Department Department of Molecular Biology and Department of Genetics
Lab Lee Lab
Street address 185 Cambridge Street
City Boston
State/province Massachusetts
ZIP/Postal code 02114
Country USA
 
Platform ID GPL13112
Series (2)
GSE118919 Transcriptome-wide analysis upon DCP1A knockout
GSE118943 DCP1A knockout: transcriptome-wide characterization
Relations
BioSample SAMN09881732
SRA SRX4597438

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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