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Sample GSM3528175 Query DataSets for GSM3528175
Status Public on Jun 25, 2020
Title Tsix +/- differentiation day 7 (replicate 2)
Sample type SRA
 
Source name embryonic stem cells
Organism Mus musculus
Characteristics genotype: Tsix +/-
developmental stage: differentiation day 7
Sex: female
strain: C57BL/6J x CAST/EiJ hybrid
Treatment protocol Nuclei were isolated, permeabilized for nuclear run-on. Nascent transcripts were labeled with Biotin-11-ATP, Biotin-11-CTP, Biotin-11-GTP, Biotin-11-UTP
Growth protocol Mouse ES cells were grown on gelatin coated plates in 2i+LIF-containing medium or differentiated accordingly
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using TRIzol extraction,biotin-labeled RNA was enriched using strepatividing pulldown
Library preparation is combined to PROseq experiment (three individual streptavidin enrichment steps) and was performed as described in (Kwak et al. 2013 and Mahat et al. 2016); Strand-specific RNA sequencing, multiplexed
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description ES-d7_Rep2
Data processing Adaptors were trimmed using cutadapt
Reads were aligned to mm9 genome using bowtie2 and novoalign
allele specific reads were called by custom script (Pinter et al., 2012)
Metagene analysis was done by deeptools2 (Ramirez et al., 2016) and custom python scripts
Strand-specific PRO-seq coverage files (bigwig format) were generated by using uniquely mapped reads normalized by fragments per million with deeptools
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for strand-specific (fwd:watson, rev:crick strand) and RPKM normalized
 
Submission date Dec 21, 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)
GSE118943 DCP1A knockout: transcriptome-wide characterization
GSE124289 Genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq) during female mouse ES differentiation
Relations
BioSample SAMN10637959
SRA SRX5174626

Supplementary file Size Download File type/resource
GSM3528175_ERa7-6_ES-d7_Rep2.b2def.fwd.RPKM.bw 32.3 Mb (ftp)(http) BW
GSM3528175_ERa7-6_ES-d7_Rep2.b2def.rev.RPKM.bw 31.9 Mb (ftp)(http) BW
GSM3528175_ERa7_6_ES-d7_Rep2_cas.fwd.RPKM.bw 2.6 Mb (ftp)(http) BW
GSM3528175_ERa7_6_ES-d7_Rep2_cas.rev.RPKM.bw 2.6 Mb (ftp)(http) BW
GSM3528175_ERa7_6_ES-d7_Rep2_mus.fwd.RPKM.bw 9.1 Mb (ftp)(http) BW
GSM3528175_ERa7_6_ES-d7_Rep2_mus.rev.RPKM.bw 8.8 Mb (ftp)(http) BW
GSM3528175_ERa7_6_comp.fwd.RPKM.bw 22.4 Mb (ftp)(http) BW
GSM3528175_ERa7_6_comp.rev.RPKM.bw 22.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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