|
| Status |
Public on Oct 24, 2018 |
| Title |
ATAC_DMSO-4hr |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: immortalized cervical cancer cells
treatment: DMSO
timepoint: 4hr
|
| Treatment protocol |
HeLa S3 cells were treated with DMSO or I-BRD9 (10 μM ) for 6 h prior to isolating chromatin (ChIP-seq) or induction with EGF (100 ng/ml) (ATAC-seq).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq samples were purified from sonicated nuclei using antibody-based immunoprecipitation. ATAC-seq samples were generated using Nextera transposase (Illumina) on purified nuclei.
ChIP-seq libraries were prepared using the Kapa Hyper Prep Kit according to the manufacturer's protocol. ATAC-seq libraries were prepared using Nextera chemistry (Illumina).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ATAC_nodup.tn5_pooled.filt.peaks.bed
|
| Data processing |
ATAC-seq: paired‐end 38‐bp sequencing reads were aligned with BWA (version 0.7.10) allowing one mismatch.
bam files were converted to tag align files using gawk and bedtools.
tag alignments were shifted (+4 bp for plus strand and -5bp for minus strand) to account for TN5 insertion
peak calling was done with MACS (version 2.1.0).
ChIP-seq: sequencing reads were aligned with BWA (version 0.7.10) allowing one mismatch.
bam files were converted to tag align files using gawk and bedtools.
peak calling was done with MACS (version 2.1.0).
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq fold change (vs input) signal files in bigwig format and called peaks in bed format. ATAC-seq fold change (vs. background) signal in bigwig format and called pooled peaks in bed format.
|
| |
|
| Submission date |
Oct 24, 2018 |
| Last update date |
Jan 14, 2022 |
| Contact name |
Robin Andersson |
| E-mail(s) |
robin@binf.ku.dk
|
| Organization name |
University of Copenhagen
|
| Department |
Biology
|
| Lab |
Andersson Lab
|
| Street address |
Ole Maaloes Vej 5
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE121351 |
A non-canonical GLTSCR1L-containing BAF complex mediates H3K27ac-dependent enhancer activities |
|
| Relations |
| BioSample |
SAMN10285347 |
| SRA |
SRX4928884 |
