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Sample GSM2560719 Query DataSets for GSM2560719
Status Public on Dec 31, 2019
Title WT_16h_H3K36me3
Sample type SRA
 
Source name Murine embryonic fibroblasts (MEFs)
Organism Mus musculus
Characteristics genotype/variation: WT
antibody: Anti-Histone H3 (tri methyl K36) antibody - ChIP Grade (ab9050)
strain: c57bl/6
time point: 16h
agent: none
Treatment protocol WT MEFs and NSD2 KO MEFs were treated with mouse recombinant IFNβ (100 units/ml, PBL Interferon Source) for 16h.
Growth protocol MEFs were grown in Dulbucco’s minimal essential medium (DMEM) containing 10% donor bovine serum at 37°C.
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked with 1% formaldehyde for 10 min and nuclei were pelleted after sequential wash and resuspended in sonication buffer (0.1% SDS, 1mM EDTA, 10mM Tris (pH8.1)) and sonicated in a Covaris to shear the chromatin into 200-300 bp fragments. 50ug of chromatin was immunoprecipitated using anti-H3K36me3 antibody (Abcam), anti-HA antibody (Abcam) and anti-ZMYND11 antibody (Millipore). Immunoprecipitated chromatin was de-crosslinked and DNA purified.
ChIP-seq libraries were constructed using a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). DNA sequence was performed by NextSeq system (Illumina).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model NextSeq 550
 
Description Nsd2(+/+)
Data processing deepTools(2.4.3-1)
Bamcoverage
bamCoverage --bam ${j}.bam -of bigwig -o ${j}.SeqDepthNorm.bw --binSize 10 --normalizeTo1x 2150570000 --ignoreForNormalization chrX --extendReads 150 --centerReads --smoothLength 30
Genome_build: mm9
Supplementary_files_format_and_content: bigWig
 
Submission date Mar 31, 2017
Last update date Dec 31, 2019
Contact name Mahesh Bachu
E-mail(s) bmahesh07@gmail.com, bachum@hss.edu
Organization name Hospital For Special Surgery
Street address 535 E 70th St 6th Floor
City New York
State/province New York
ZIP/Postal code 10021
Country USA
 
Platform ID GPL21626
Series (2)
GSE97277 Genome-wide analysis of H3.3, H3K36me2, H3K36me3 and ZMYND11 accumulation in WT MEFs and NSD2 KO MEFs.
GSE97280 NSD2 negatively regulate innate immune response through Zmynd11
Relations
BioSample SAMN06671913
SRA SRX2692881

Supplementary file Size Download File type/resource
GSM2560719_WT_16h_ZMYND11_S11_R1_sorted.SeqDepthNorm.bw 269.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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