|
| Status |
Public on Mar 14, 2017 |
| Title |
DMSO_H3K4me3_A |
| Sample type |
SRA |
| |
|
| Source name |
L3.6_DMSO_H3K4me3
|
| Organism |
Homo sapiens |
| Characteristics |
immortalization type: SV40 large T antigen immortalized
cell line: L3.6
chip antibody (company, cat.#, clone): Diagenode, C15410003
|
| Treatment protocol |
Cells were treated with DMSO or 4SC-202 (1 µg/ml) for 24 hours
|
| Growth protocol |
L3.6 cells were maintained in Minimum Essential Media (MEM, Invitrogen) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Sigma-Aldrich) as previously described (Herreros-Villanueva et al., 2013).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The ChIP was performed with 10 min crosslinking in 1 % formaldehyde in PBS. Following chromatin shearing , 1-2µg antibody was used for immunoprecipitation overnight. The immunocomplexes were incubated 2 additional hours with protein A sepharose beads and subjected to washes. After reversing the cross-linking, the DNA was isolated by standard phenol-chloroform-isoamyl extraction procedure.
ChIP-Seq libraries were prepared with MicroPlex Library Preparation Kit following the manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ChIP DNA
processed data file: Merged_DMSO_H3K4me3.bigwig
|
| Data processing |
The FASTQ files were mapped to the human reference genome (assembly hg19) using BOWTIE2 with very-sensitive presets in end-to-end mode on Galaxy Platform (version 2.2.6). The resulting BAM files of ChIPs were deduplicated with RmDup Samtools (Galaxy version 2.0). The corresponding BAM files of the replicates were merged. The merged BAM files were normalized to fragments (reads) per kilobase per million (RPKM) using the bamCoverage tool on Deeptools Galaxy (version 1.1.4) with removal of duplicates (ignoreDuplicates).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig represent the normalized RPKM values of ChIP-seq signal
|
| |
|
| Submission date |
Nov 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Steven A. Johnsen |
| Organization name |
University Medical Center Goettingen
|
| Department |
Department of General, Visceral and Pediatric Surgery
|
| Lab |
AG Johnsen/Tumorepigenetics
|
| Street address |
Robert-Koch-Straße 40
|
| City |
Goettingen |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE90110 |
Functional genomics of HDAC class-I specific inhbitor 4SC-202 in pancreatic cell lines [ChIP-seq] |
| GSE90112 |
Functional genomics of HDAC class-I specific inhbitor 4SC-202 in pancreatic cell lines |
|
| Relations |
| BioSample |
SAMN06045344 |
| SRA |
SRX2365613 |
