|
| Status |
Public on Jul 07, 2023 |
| Title |
HCT-8_DMSO_4h_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HCT-8 cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT-8
disease: colon carcinoma
treatment: DMSO_4h
replicate: rep2
ID: BI-VIE-0000-0000-0007-8604
source_id: J14001
|
| Treatment protocol |
See samples section.
|
| Growth protocol |
The cell lines were grown in the media recommended by the vendor.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed in TRI lysis reagent (Qiagen, #79306) according to the manufacturer's instructions. Total RNA was isolated with RNAeasy Mini Kit (Qiagen, #73404).
Quant-seq libraries were prepares using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina from Lexogene (#015.96) according to manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Multiplexed samples were sequenced on an Illumina NextSeq 500 system. Base-calling was performed using the Real-Time Analysis (RTA) software version 2.4.11. Conversion of the raw bcl2 output files to gzipped FASTQ files was performed using the bcl2fastq2 software version 2.20.0 provided by Illumina.
Data was processed with a pipeline building upon the implementation of the ENCODE "Long RNA-seq" pipeline: In brief, single-end sequencing reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (source 1000 Genomes Project - GRCh38_full_analysis_set_plus_decoy_hla.fa, excluding alternate contigs, chromosome mapping via grch38_ucsc2ensembl.txt) using the STAR (v2.5.2b) aligner allowing for soft clipping of adapter sequences. For quantification, transcript annotation files from Ensembl version 86 were used. Samples were quantified with the above annotations using featureCount (v1.5.1). Quality controls were implemented using FastQC (v0.11.5), picardmetrics (v0.2.4), and dupRadar (v1.0.0) at the respective steps. Finally, differential expression analysis was performed on the counts derived from featureCount using limma/voom.
Assembly: GRCh38
Supplementary files format and content: Processed data files contain sample-wise results produced by FeaturesCounts and include raw count values for each gene.
|
| |
|
| Submission date |
Aug 04, 2022 |
| Last update date |
Jul 08, 2023 |
| Contact name |
Daniel Gerlach |
| E-mail(s) |
daniel.gerlach@boehringer-ingelheim.com
|
| Organization name |
Boehringer Ingelheim RCV GmbH & Co KG
|
| Department |
Global Computational Biology and Digital Sciences
|
| Street address |
Dr.-Boehringer-Gasse 5-11
|
| City |
Vienna |
| ZIP/Postal code |
1121 |
| Country |
Austria |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE210540 |
GDF15 gene suppression by BET inhibition and gene signature based personalized chemotherapy to counteract cachexia [Quant-seq] |
| GSE210542 |
GDF15 gene suppression by BET inhibition and gene signature based personalized chemotherapy to counteract cachexia |
|
| Relations |
| BioSample |
SAMN30152160 |
| SRA |
SRX16846926 |
