|
| Status |
Public on Mar 22, 2023 |
| Title |
A549 parental rep3 |
| Sample type |
SRA |
| |
|
| Source name |
A549 parental
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
cell type: lung adenocarcinoma
treatment: NA, no IFN-gamma
genotype: parental
|
| Treatment protocol |
IFN-gamma of 10/ml ng or 100 ng/ml for 48h
|
| Growth protocol |
DMEM + 10 % p/s & 1% FBS. Seeded before confluency
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Roche High Pure RNA Isolation Kit
Standard Illumina RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
NT_3
|
| Data processing |
Nextseq500 base calling
Hisat2 for alignment with hg19
Raw counts with Homer -condensed
Generation of counts with Homer analyzeRepeats.pl rna hg19 -noadj -condenseGenes -count gene
Genome_build: hg19
Supplementary_files_format_and_content: A549_counts.txt (raw counts for A549 mock, knockout and parental)
Supplementary_files_format_and_content: IFNy_A549_counts.txt (raw counts for A549 mock and knockout +/- IFN-gamma (10 and 100 ng/ml))
|
| |
|
| Submission date |
Nov 29, 2021 |
| Last update date |
Mar 22, 2023 |
| Contact name |
Anna-Liisa Levonen |
| Organization name |
University of Eastern Finland
|
| Department |
A.I. Virtanen Institute
|
| Lab |
ALL
|
| Street address |
Neulaniementie 2
|
| City |
Kuopio |
| State/province |
Savonia region |
| ZIP/Postal code |
70211 |
| Country |
Finland |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE189804 |
A549 NRF NT, mock and knockout RNAseq |
|
| Relations |
| BioSample |
SAMN23492196 |
| SRA |
SRX13255365 |
