|
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 |