|
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 |