|
Status |
Public on Oct 25, 2016 |
Title |
A549 - Ctrl siRNA-1 - rep1 |
Sample type |
SRA |
|
|
Source name |
A549 lung cancer cell line - Ctrl siRNA-1 - rep1
|
Organism |
Homo sapiens |
Characteristics |
cell line: A549 cell type: Human lung adenocarcinoma cell line
|
Treatment protocol |
250,000 cells were transfected with Lipofectamine RNAiMAX reagent containing 5 nmol siRNA particles in a 6-well plate. Three transfections siRNAs targeting NFE2L2 were performed, using three independent duplexes, while four control transfections were done using two different control duplexes.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was prepared using the RNeasy Mini kit. 8 strand-specific total RNA-seq libraries were generated using TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Reads were aligned to hg19 genome using Hisat version 0.1.6-beta. Number of reads mapping to each feature were calculated using htseq-count version 0.6.0. Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files including raw counts for each sample.
|
|
|
Submission date |
Nov 27, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Arghavan Ashouri |
E-mail(s) |
arghavan.ashouri@gu.se
|
Organization name |
University of Gothenburg
|
Department |
Medical Biochemistry and Cell Biology
|
Street address |
Medicinaregatan 9A
|
City |
Gothenburg |
ZIP/Postal code |
41390 |
Country |
Sweden |
|
|
Platform ID |
GPL18573 |
Series (1) |
GSE75452 |
Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events |
|
Relations |
BioSample |
SAMN04201507 |
SRA |
SRX1453413 |