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Sample GSM2872482 Query DataSets for GSM2872482
Status Public on Sep 27, 2018
Title H3K4me3_KO-2_-RA
Sample type SRA
 
Source name embryonal carcinoma cell line
Organism Homo sapiens
Characteristics cell line: NT2/D1
cell type: pluripotent embryonal carcinoma cell line
genotype/variation: CRISPR/Cas9-mediated deletion of PRMT6
atra: -
chip antibody: H3K4me3 (07-473, Merck Millipore)
Treatment protocol 1 µM all-trans retinoic acid (ATRA) for 3 days.
Growth protocol NT2/D1 cells were cultured in DMEMI supplemented with 10% FCS.
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked in the presence of 1% formaldehyde. Cell lysates were sonicated and Protein-DNA complexes were enriched by immunoprecipitation with mentioned antibodies.
Libraries were prepared according to the manufacturer’s protocol (Diagenode, MicroPlex Library Preparation Kit).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Description CRISPR/Cas9-mediated deletion of PRMT6 in NT2/D1 cells.
Data processing Illumina RTA 1.8.66.4 software used for basecalling.
Sequenced reads were trimmed for adaptor using Illumina bcl2fastq, then mapped to hg19 whole genome using bowtie2.
Aligned files (bam) were filtered for duplicated aligned reads.
MACS 1.4 was used to perform the peak calling.
Peaks were filtered using criteria; minimum 35 tags and 2 fold above IgG; peak length/tag count <= 15.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig files generated using deeptools2 bamCoverage function.
Supplementary_files_format_and_content: *peaks.txt.: Tab-delimited text; Peak files incorporate the number of peaks after filtering for given sample.
 
Submission date Dec 01, 2017
Last update date May 15, 2019
Contact name Uta Maria Bauer
E-mail(s) bauer@imt.uni-marburg.de
Organization name Philipps University Marburg
Department Institute of Molecular Biology and Tumor Research
Lab AG Bauer
Street address Hans-Meerwein-Str. 2
City Marburg
State/province Hessen
ZIP/Postal code 35043
Country Germany
 
Platform ID GPL18460
Series (2)
GSE107609 Genomic occurrence analysis of PRMT6-dependent H3R2me2a
GSE107612 Genomic location of PRMT6-dependent H3R2 methylation is decisive for the transcriptional outcome of associated genes
Relations
BioSample SAMN08120266
SRA SRX3437590

Supplementary file Size Download File type/resource
GSM2872482_H3K4me3_KO-2_-RA.bw 103.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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