|
| Status |
Public on Apr 09, 2024 |
| Title |
Hela Camptothecin (10 µM), 24h, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Cervix
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Cervix
cell line: HeLa
cell type: epithelial cell
genotype: ATCC CCL-2
treatment: Camptothecin 24h
|
| Treatment protocol |
TRAIL 24 h treatment (30 ng/ml), Camptothecin 24h treatment (10 µM), or Doxorubicin 24h treatment (2 µM)
|
| Growth protocol |
HeLa cells were maintained in DMEM GlutaMAX supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNeasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
We have prepared sequencing libraries from your 16 samples using the Truseq stranded mRNA library preparation method from Illumina
RNAseq. Paire-end. 150 bp
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
In this workflow, reads are aligned to a reference genome using HISAT2. From these alignment, the number of alignments per gene are then quantified.
In essence this workflow contains 3 steps per sample, namely read trimming, alignment ans quantification.
In the trimming Illumina adapter and poly-A sequences are removed from the reads. The trimmed reads are then aligned using HISAT2 (Kim et al, 2019).
After the HISAT2 alignment, quantification is performed using HT-Seq count
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include counts values for each Sample
|
| |
|
| Submission date |
Apr 14, 2023 |
| Last update date |
Apr 09, 2024 |
| Contact name |
Francisco José Iborra |
| E-mail(s) |
[email protected]
|
| Organization name |
Instituto de Biomedicina de Valencia (CSIC)
|
| Street address |
C/ JAIME ROIG, 11
|
| City |
Valencia |
| State/province |
Valencia |
| ZIP/Postal code |
46010 |
| Country |
Spain |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE229761 |
Chemotherapy induces cell plasticity; controlling plasticity increases therapeutic response. |
|
| Relations |
| SRA |
SRX19972657 |
| BioSample |
SAMN34191252 |
