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Sample GSM3273422 Query DataSets for GSM3273422
Status Public on Sep 27, 2018
Title NT2D1_KO_H3R2me2a_+Doxy_R1
Sample type SRA
 
Source name NT2D1_KO_H3R2me2a_+Doxy
Organism Homo sapiens
Characteristics cell line: NT2/D1
cell type: embryonal carcinoma cell line
cell status: pluripotent
genotype/variation: CRISPR/Cas9-mediated deletion of PRMT6 in NT2/D1 cells and PRMT6 re-expression with doxy
chip antibody: rat monoclonal generated in the laboratory
Treatment protocol 1 µM all trans retinoic acid (ATRA) for 3 days; 16 µM MS049 (PRMT6 inhibitor) 3 days; PRMT6 rescue with Doxy treatment 6 days
Growth protocol NT2/D1 and U2OS 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 sonified 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 103_B6Flp_ChIPP6_IP_260218_CTTGTA
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
Supplementary_files_format_and_content: bigwig files generated using deeptools2 bamCoverage function with binsize=50, peak files incorporate the number of peaks after filtering for given sample; bigwig files were normalized with CPM
 
Submission date Jul 17, 2018
Last update date Sep 27, 2018
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)
GSE107612 Genomic location of PRMT6-dependent H3R2 methylation is decisive for the transcriptional outcome of associated genes
GSE117200 Genomic location of PRMT6-dependent H3R2 methylation is decisive for the transcriptional outcome of associated genes [ChIP-seq]
Relations
BioSample SAMN09668444
SRA SRX4397524

Supplementary file Size Download File type/resource
GSM3273422_NT2D1_KO_H3R2me2a_+Doxy_R1normCPM.bw 150.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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