|
| Status |
Public on Oct 25, 2016 |
| Title |
A549 - Mock transfection control |
| Sample type |
SRA |
| |
|
| Source name |
A549 lung cancer cell line - Mock transfection
|
| 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 |
SAMN04201454 |
| SRA |
SRX1453409 |
