|
| Status |
Public on May 17, 2019 |
| Title |
Control_siRNA_TNFalpha+_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
HCC95 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCC95 cells
treatment: TNFalpha treated
RNAi: control
|
| Treatment protocol |
For ALAL-1 inhibition, 200,000 HCC95 cells per well were plated in a 6-well plate. The next day siRNAs at a final concentration of 30 nM siRNA were transfected using Lipofectamine 2000 (Invitrogen) following manufacturers protocol. The TNFalpha treatment was performed using a concentration of 10 ng/ml (R&D systems) for 4 hours.
|
| Growth protocol |
HCC95 cells were cultured at 37ºC in the presence of 5% CO2 using RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% of pen strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from HCC95 cells was extracted using Maxwell® 16 Total RNA Purification Kit (Promega). Triplicates for each condition (ALAL-1 inhibition, TNFalpha treatment and controls) were performed. RNA quality was assessed using Agilent 2200 TapeStation.
RNA-seq libraries were prepared following the Illumina TruSeq Stranded mRNA Library Prep protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
The generated BCL files were demultiplexed using bcl2fastq conversion software (version 2.17)
Quality control of the obtained reads was performed using fastqc and Trimmomatic
Filtered reads were mapped to the hg19 version using bowtie2
Read summarization was done with the featureCounts program and using the gencode.v19.hg19.gtf annotation
Differential gene expression was performed using the R package DESeq2.
Genome_build: hg19
|
| |
|
| Submission date |
May 18, 2018 |
| Last update date |
May 17, 2019 |
| Contact name |
Maite Huarte |
| E-mail(s) |
[email protected]
|
| Organization name |
CIMA
|
| Street address |
c/ Avd Pio XII, 55
|
| City |
Pamplona |
| State/province |
Navarra |
| ZIP/Postal code |
31008 |
| Country |
Spain |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE114632 |
Analysis of copy number alterations from a lncRNA perspective reveals ALAL-1 a mediator of NSCLC immune evasion. |
|
| Relations |
| BioSample |
SAMN09223581 |
| SRA |
SRX4099421 |
