|
| Status |
Public on Oct 17, 2018 |
| Title |
DMSO_0min_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: immortalized cervical cancer cells
treatment: DMSO
timepoint: 0
|
| Growth protocol |
HeLa S3 cells were grown on 60 mm plates treated with DMSO or I-BRD9 (10 μM ) 6 h prior to induction with EGF (100 ng/ml) for 30 min
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRI Reagent® (Ambion) according to manufacturer’s recommendations
CAGE libraries were prepared using the protocol by (Takahashi et al. 2012) with an input of 3 μg of total RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
CAGE-seq: assigned reads were 5′-end trimmed to remove linker sequences (9+2 bp to account for the CAGE protocol G-bias), 3′-end trimmed to a length of 25 bp using FASTX toolkit (version 0.0.13)
Reads matching to reference rRNA sequences were discarded using rRNAdust
mapping to the human genome was performed using BWA (version 0.7.10)
Only the 5’ ends of mapped reads were considered in subsequent analyses.
Genome_build: hg19
Supplementary_files_format_and_content: CAGE tag files in bed format.
|
| |
|
| Submission date |
Oct 16, 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 |
GPL11154 |
| Series (1) |
| GSE121351 |
A non-canonical GLTSCR1L-containing BAF complex mediates H3K27ac-dependent enhancer activities |
|
| Relations |
| BioSample |
SAMN10247760 |
| SRA |
SRX4893405 |
