|
| Status |
Public on Sep 01, 2022 |
| Title |
HAP1_RNA-seq_ARID1A_dCHAF1A_12h_r5 |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Homo sapiens |
| Characteristics |
library: RNA-seq
cell line: HAP1
replicate: 5
knockout: ARID1A
degradation: CHAF1A
drug_treatment: dTAG 12h
|
| Growth protocol |
HAP1 WT and knock-out cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM, Thermo Fisher Scientific, 21980-032) supplemented with 10% heat inactivated Fetal Bovine Serum (FBS, Thermo Fisher Scientific, 10500) and 1% Pen Strep (100 units/ml Penicillin, 100 µg/ml Streptomycin, Thermo Fisher Scientific, 15140-122). A549 cells were cultured in F-12K Nut Mix (Thermo Fisher Scientific, 21127-022) supplemented with 10% FBS and 1% Pen Strep.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated with RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
RNA-seq for HAP1 cell line with ARID1A knockout and degradation of CHAF1A for 12 hours, replicate 5
|
| Data processing |
Reads were trimmed with Trimmomatic, aligned to the GRCh37/hg19 human genome assembly using Bowtie1 and quantified transcript isoforms from Ensembl version 75 using BitSeq with default parameters. Read counts per gene are the maximum counts per isoform.
Genome_build: hg19
Supplementary_files_format_and_content: CSV file contains read counts for each sample for each gene
|
| |
|
| Submission date |
Jan 17, 2019 |
| Last update date |
Sep 01, 2022 |
| Contact name |
Christoph Bock |
| E-mail(s) |
cbock@cemm.oeaw.ac.at
|
| Organization name |
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
|
| Street address |
Lazarettgasse 14
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE125219 |
Histone chaperone CAF-1 is a synthetic lethal vulnerability in the context of ARID1A deficiencies [RNA-Seq] |
| GSE125221 |
Histone chaperone CAF-1 is a synthetic lethal vulnerability in the context of ARID1A deficiencies |
|
| Relations |
| BioSample |
SAMN10764626 |
| SRA |
SRX5258189 |
