|
| Status |
Public on Sep 04, 2020 |
| Title |
Ctrl_6h-1 |
| Sample type |
SRA |
| |
|
| Source name |
PeTa_Ctrl_6h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PeTa
cell type: Merkel cell carcinoma cell line
treatment: DMSO
4su labeling time before harvest (min): 360
|
| Treatment protocol |
Cells were pre-treated with GSK-LSD1 inhibitor for 30min and 4SU labeling of newly synthesized transcripts was performed for 60 or 360min.
|
| Growth protocol |
Cells were cultured as suspension cells in RPMI-1640 supplemented with 10% FBS, 2 mM L-glutamine, 50 U/mL penicillin and 50 mg/mL streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation from cells was performed with an in-house paramagnetic bead-based purification protocol.
3'UTR sequencing libraries were generated from 500ng total RNA using a commercial kit (QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
library strategy: SLAMseq (Thiol (SH)-Linked Alkylation for the Metabolic sequencing of RNA)
Reads were aligned against the human genome (hg38) with STAR.
reads were processed using SlamDunk v0.2.4 running the full analysis procedure (slamdunk all) and stringency filter set to 2 (requiring ≥ 2 T>C conversions per read)
For details see: http://t-neumann.github.io/slamdunk/docs.html
Genome_build: hg38
Supplementary_files_format_and_content: TSV table containing UTR coordinates named by EntrezID, raw and normalized read counts, as well as T>C conversion statistics.
|
| |
|
| Submission date |
Mar 31, 2020 |
| Last update date |
Sep 05, 2020 |
| Contact name |
Anna Obenauf |
| Organization name |
IMP - Research Institute of Molecular Pathology
|
| Lab |
Anna Obenauf
|
| Street address |
Campus-Vienna-Biocenter 1
|
| City |
Vienna |
| State/province |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE147816 |
Transcriptomic maps of pharmacological LSD1 inhibition in MCC [SLAMseq] |
| GSE147817 |
Pharmacological LSD1 inhibition in MCC |
|
| Relations |
| BioSample |
SAMN14501406 |
| SRA |
SRX8036473 |
