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Sample GSM1645696 Query DataSets for GSM1645696
Status Public on Jun 17, 2015
Title Abl1_H3K27me3_ChIPSeq
Sample type SRA
 
Source name B-lymphoid clonal cell line Abl1 / S1Cs-A5
Organism Mus musculus
Characteristics strain: 129S1/SvImJ x CAST/EiJ F1
Sex: female
cell type: B-lymphoid immortalized with Abelson murine leukemia virus
chip antibody: Anti-H3K27me3 (ABE44 Millipore, Billerica, MA)
Treatment protocol No treatment.
Growth protocol Cells were grown at 37°C in presence of 5% CO2, in RPMI complemented with 20% FBS, 1X Penicillin-Streptomycin-Glutamine (Gibco 10378-016) and 1X GlutaMAX Supplement (Gibco 35050-061).
Extracted molecule genomic DNA
Extraction protocol Chromatin immunoprecipitation (ChIP) on clonal cell line Abl.1 was performed as previously described (Nag et al. Elife. 2013 Dec 31;2:e01256). Briefly, cells were fixed with 1% formaldehyde for 5 minutes at 37°C. Fragmentation was performed using Covaris sonicator. An aliquot of sheared chromatin was saved as input control. Immunoprecipitation was performed with Anti-H3K27me3 antibody (ABE44 Millipore, Billerica, MA) and anti-H3K36me3 antibody (AB9050, Abcam, Cambridge, MA and UK), using Protein-A Sepharose beads.
ChIP-Seq libraries were prepared using NEBNext ChIP-Seq library prep reagent set for Illumina (NEB E6200S) following manufacturer’s instructions. Barcoded libraries were sequenced using Illumina HiSeq platform (SE50).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Cell line is described in Zwemer et al. (Genome Biol. 2012 Feb 20;13(2):R10).
Data processing The H3K27me3, H3K36me3 and input control reads were mapped to the mm9 genome using Bowtie 2 with default parameters (Langmead B, Salzberg SL. Nat Methods. 2012 Mar 4;9(4):357-9). Library sizes were of 32, 46 and 57 million unique reads, respectively, with alignment rate of 92% in each case.
Duplicate reads were removed.
Genome_build: mm9
Supplementary_files_format_and_content: wig
 
Submission date Mar 27, 2015
Last update date May 15, 2019
Contact name Sebastien Vigneau
E-mail(s) sebastien_vigneau@dfci.harvard.edu
Phone +1-857-540-5439
Organization name Dana-Farber Cancer Institute
Department Cancer Biology
Lab Alexander Gimelbrant
Street address 450 Brookline Avenue
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL13112
Series (2)
GSE67380 Chromatin signature identifies monoallelic gene expression across mammalian cell types (ChIP-seq)
GSE67384 Chromatin signature identifies monoallelic gene expression across mammalian cell types
Relations
BioSample SAMN03450225
SRA SRX971602
Named Annotation GSM1645696_Abl1_H3K27me3.wig.gz

Supplementary file Size Download File type/resource
GSM1645696_Abl1_H3K27me3.wig.gz 8.6 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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