|
| Status |
Public on Nov 10, 2020 |
| Title |
H3K36me3 no 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 |
SAMN14056049 |
| SRA |
SRX7692248 |
