|
| Status |
Public on Jun 20, 2024 |
| Title |
HEK293T cells, control siPOOL repllicate 4b |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
cell type: Human embryonic kidney
treatment: ctrl siPOOL
|
| Treatment protocol |
Depletions were performed for 72 hours. siPOOLs were transfected to a final concentration of 5nM with RNAiMax
|
| Growth protocol |
HEK293T cells were maintained in DMEM supplemented with 10% fetal calf serum (FCS) and antibiotics in a humidified atmosphere with 5% CO2 at 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by Phenol/Chloroform extraction. 1ug of RNA was used for library preparation.
Ribosomal RNAs were depleted and sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
negctrl_4b
|
| Data processing |
in-house snakemake RNAseq analysis pipeline
FastQC quality control
Cutadapt adapter timming
STAR alignment usiing the parameters: -outFilterMulitmapNmax 20 -quantMode GeneCounts
Assembly: hg38
Supplementary files format and content: bam files include aligned reads for each sample
Supplementary files format and content: Tab-separated value file includes raw read counts for each
|
| |
|
| Submission date |
Jun 01, 2023 |
| Last update date |
Jun 20, 2024 |
| Contact name |
Stefanie Jonas |
| E-mail(s) |
stefanie.jonas@mol.biol.ethz.ch
|
| Organization name |
ETH Zurich
|
| Department |
Biology
|
| Street address |
Otto-Stern-Weg 5
|
| City |
Zürich |
| State/province |
Zürich |
| ZIP/Postal code |
8093 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE233957 |
Basis of gene-specific transcription regulation by the Inegrator Complex (RNA-Seq) |
| GSE233958 |
Basis of gene-specific transcription regulation by the Inegrator Complex |
|
| Relations |
| BioSample |
SAMN35561964 |
| SRA |
SRX20572280 |
