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Sample GSM4301090 Query DataSets for GSM4301090
Status Public on Nov 10, 2020
Title H3K36me3 3d dox
Sample type SRA
 
Source name HEK293 cell line
Organism Homo sapiens
Characteristics antibody: H3K36me3
antibody vendor/amount: ab9050 (3.5 µg)
cell line: HEK293
Treatment protocol For induction of the ZnF-3AC construct, cell culture medium was supplemented with 1 µg/ml doxycyclin (Sigma-Aldrich) for three days.
Extracted molecule genomic DNA
Extraction protocol For ZnF(3xHA)-ChIP, chromatin was crosslinked with 1% formaldehyde, sheared using a probe sonicator (100 - 1000 bp fragment size) and preciptated with an antibody. In case of nChIP experiments, chromatin was fragmented by Mnase digest and precipitated with an antibody.
Libraries for all samples (except H3K27ac) were constructed by the Max Planck-Genome-centre Cologne. In case of H3K27ac, libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer's protocol.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 3000
 
Data processing Data were submitted in FASTQ format and all data processing steps were performed on the European Galaxy platform (usegalaxy.eu)
The quality of the reads was checked using the FastQC tool
Reads were mapped on human genome 19 (hg19/GRCh37) using bowtie2 in default settings. When necessary (re-sequencing), BAM- files were merged using the Merge BAM Files tool.
Coverage files (bigwig) were generated using bamCoverage from DeepTools (25 bp bins) with RPKM normalization. Re-calibration of bigWig files was performed as described in the supplement section to obtain a scaling factor for. BamCoverage was repeated in RPKM mode (25 bp bins) implying this scaling factor.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bigWig
 
Submission date Feb 07, 2020
Last update date Nov 11, 2020
Contact name Albert Jeltsch
E-mail(s) albert.jeltsch@ibc.uni-stuttgart.de
Phone +49 685 64390
Organization name University Stuttgart
Department Institute of Biochemistry and Technical Biochemistry
Street address Allmandring 31
City Stuttgart
ZIP/Postal code 70569
Country Germany
 
Platform ID GPL21290
Series (2)
GSE144904 Genome-wide investigation of the dynamic changes of epigenome modifications after DNA methylation editing
GSE144928 Genome-wide investigation of the dynamic changes of epigenome modifications after DNA methylation editing [ChIP-Seq]
Relations
BioSample SAMN14056048
SRA SRX7692249

Supplementary file Size Download File type/resource
GSM4301090_H3K36me3_3d_dox_1.19x_.bigwig 89.7 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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