|
| Status |
Public on Jul 01, 2019 |
| Title |
DHX36-KO cPDS-RNA-seq 3 |
| Sample type |
SRA |
| |
|
| Source name |
DHX36-KO-HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
genotype/variation: CRISPR/Cas9-mediated DHX36 Knockout
passages: 15 - 20
treated with: 2 µM carboxyPyridostatin (cPDS)
|
| Treatment protocol |
42 h before harvesting, cells were treated with 2 µM cPDS
|
| Growth protocol |
HEK293 cells and DHX36-KO-HEK293 were grown and routinely passaged in DMEM supplemented with 10% FCS and 1% pen/strip.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Trizol.
Library was constructed using the NEBnext Ultra Directionsal RNA Library Prep Kit for Illumina with rRNA depletion
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
6_KO_cPDS_RNAseq
processed data file:
PDS_WT_vs_KO_gene_exp.diff
PDS_WT_vs_PDS_KO_gene_exp.diff
WT_vs_PDS_KO_gene_exp.diff
|
| Data processing |
Illumina HiSeq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the hg19 genome using TopHat
Genome_build: hg19
Supplementary_files_format_and_content: cuffdiff output
|
| |
|
| Submission date |
Oct 19, 2017 |
| Last update date |
Jul 01, 2019 |
| Contact name |
Markus Sauer |
| E-mail(s) |
markus.sauer@stud-mail.uni-wuerzburg.de
|
| Organization name |
University of Würzburg
|
| Street address |
Am Hubland, Biozentrum - Lehrstuhl für Biochemie
|
| City |
Würzburg |
| ZIP/Postal code |
97074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE105170 |
DHX36 resolves G-rich structures in mRNA untranslated region to allow their translation [cPDS-RNA-seq] |
| GSE105175 |
DHX36 resolves G-rich structures in mRNA untranslated region to allow their translation |
|
| Relations |
| BioSample |
SAMN07814401 |
| SRA |
SRX3301059 |
