|
| Status |
Public on Feb 18, 2019 |
| Title |
ChIP_H3K27ac_A375 |
| Sample type |
SRA |
| |
|
| Source name |
Melanoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A375
time point: Base line
|
| Growth protocol |
Cells were kept at 37°C, with 5% CO2 and were maintained in Ham's F10 nutrient mix (Thermo Fished Scientific) supplemented with 10% fetal bovine serum (FBS; Invitrogen) and 100 µg ml-1 penicillin/streptomycin (Thermo Fished Scientific).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was extracted using the MagnaChIP-seq kit (millipore). 4 µg of antibody was used on 2 million cells. Sonication was performed for 12 cycles, 30 sec pulses using the biorupter.
Illumina TruSeq
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
ChIP_H3K27ac_A375.nofirst5bp.minMQ4.sorted.bw
|
| Data processing |
Reads obtained from H3K27Ac ChIP-seq were mapped to the genome using Bowtie2 (v2.1.0). The sensitive-local setting for Bowtie2 was used to correct for a high percentage of mismatches at the start of a read. bigWig files were generated from bam files using BEDTools (v2.17.0) and the scores represent the coverage. We used as control the merged control profiles of five cell lines, namely A375, MM011, MM032, MM047 and MM057. We used MACS2 (v2.0.10) with the command 'callpeak -t ChIPseq_file -c Control_file -g hs --qvalue 0.001 -n name'.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from bam files using BEDTools (v2.23.0) and the scores represent the coverage. Bedfiles supplied with FDR0.001.
|
| |
|
| Submission date |
May 16, 2018 |
| Last update date |
Feb 18, 2019 |
| Contact name |
Stein Aerts |
| E-mail(s) |
stein.aerts@kuleuven.vib.be
|
| Organization name |
KU Leuven
|
| Street address |
O&N4 Herestraat 49 PO Box 602
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE114557 |
cisTopic: cis-regulatory topic modelling on single-cell ATAC-seq data |
|
| Relations |
| BioSample |
SAMN09216360 |
| SRA |
SRX4091683 |
