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Sample GSM2284171 Query DataSets for GSM2284171
Status Public on Oct 28, 2016
Title ATAC-ControlClone-Rep1
Sample type SRA
 
Source name F1 2-1 129/Castaneus Female mESCs
Organism Mus musculus
Characteristics cell type: embryonic stem cell
cell line: ControlClone
gender: female
Growth protocol Male ES cells were grown on plates coated with 0.2% gelatin and 3.5 ug/mL laminin in serum-free 2i/LIF media composed as follows: 1:1 mix of DMEM/F-12 (Gibco) and Neurobasal (Gibco) supplemented with 1X N2 (Gibco), 0.5X B-27 (Gibco 17504-044), 2 mg/mL bovine insulin (Gemini BioSciences), 1.37 ug/mL progesterone (Sigma), 5 mg/mL BSA Fraction V (Gibco), 0.1 mM 2-mercaptoethanol (Sigma), 5 ng/mL murine LIF (GlobalStem), 0.1 uM PD0325901 (Axon Medchem 1408) and 0.3 uM CHIR99021 (University of Dundee Division of Signal Transduction Therapy).
Extracted molecule genomic DNA
Extraction protocol p(A)+ RNA-seq with hybrid selection: We generated RNA sequencing libraries as described in Engreitz et al. Cell 2014. We performed hybrid selection after barcoding of DNA libraries on a combined pool as described in Gnirke et al. Nature Biotech 2009. ATAC-Seq: We performed ATAC-Seq as previously described (Buenrostro JD et al. Nature Methods 2013) using 50,000 mESCs. PRO-Seq: We performed PRO-Seq essentially as described in Kwak H et al. Science 2013. ChIP-Seq: We performed ChIP-Seq as described in Busby M et al. biorXiv 2016.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description ATAC-Seq
Data processing Library strategy: ATAC-Seq
DNA sequencing (ATAC-Seq) and RNA sequencing (PRO-Seq and RNA-seq) analyses were performed as previously described (Engreitz et al. Cell 2014) except that data were initially aligned to both the 129S1 and Castanets genomes and reads were merged using pysuspenders. For RNA-seq experiments, reads mapping to specifically to the 129 or Castaneus alleles were counted for each gene (including any read overlapping an intron or exon)
Genome_build: mm9
Supplementary_files_format_and_content: TDF: Coverage at 5bp resolution across genome for use with the Integrated Genomics Viewer (https://www.broadinstitute.org/igv/)
Supplementary_files_format_and_content: BED: Read counts mapping specifically to the 129 or Castaneus alleles. Columns: chromosome, start, end, gene, count-129, count-castaneus
 
Submission date Aug 18, 2016
Last update date May 15, 2019
Contact name Jesse Engreitz
Organization name Broad Institute
Street address 415 Main Street
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL17021
Series (1)
GSE85798 Local regulation of gene expression by lncRNA promoters, transcription, and splicing
Relations
BioSample SAMN05590788
SRA SRX2032485

Supplementary file Size Download File type/resource
GSM2284171_ATAC-ControlClone-Rep1.tdf 99.3 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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