|
| Status |
Public on Mar 28, 2019 |
| Title |
CDKN2A-NNK-1_SFL |
| Sample type |
SRA |
| |
|
| Source name |
AALE_CDKN2A_NNK
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: AALE
cell type: immortalized human bronchial epithelial cells (AALE)
genotypic perturbation: CDKN2A
genotypic perturbation type: knockout
chemical perturbation: NNK
|
| Treatment protocol |
Cell culture media was replaced, and compounds added at a concentration of 24 μg/ml CSC, 173μM BaP, 490μM NNK or DMSO. NNK and BaP compounds were obtained from Sigma-Aldrich (St. Louis MO) and CSC obtained from Murty Pharmaceuticals (Lexington, KY). Genotypic perturbations included CRISPR knockouts of FAT1, and CDKN2A, as well as overexpression of NRF2 (NFE2L2), FGFR1, NRG1 and PIK3CA. Cells transfected with a pSpCas9-EGFP (GFP) plasmid (PX458) in the absence of sgRNAs were used as controls for the CRISPR perturbations while overexpression of an empty vector containing the reporter HcRed served as control for the overexpression experiments.
|
| Growth protocol |
Cells were subcultured using Clonetics ReagentPack subculture reagents (Lonza, Portsmouth NH). In preparation for exposure, cells were plated into 24-well plates and allowed to reach confluency for 24 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using a standard Qiazol and Qiacube protocol from Qiagen (Valencia, CA).
The dual-barcoded SFL libraries were pooled from 96 individual samples and then sequenced on the Illumina® NextSeq 550 to generate more than 400 million Single-Read 75-bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Adapter sequences were trimmed from raw sequence files using Cutadapt v1.12
Quality assessment of trimmed SFL sequence files as well as raw full coverage RNA-seq sequencing files was performed with FastQC v0.11.5
Reads were aligned to human genome (UCSC RefSeq hg19) with STAR v2.5.2b
Expression quantification in RefSeq genes was carried out with featureCounts (subread) v1.5.0
Genome_build: UCSC RefSeq hg19
Supplementary_files_format_and_content: Tab-delimited text files contain two columns: (1) HGNC symbols (2)Read Counts. File names are denoted by the nomencalture {genotypic perturbation}-{chemical perturbation}-{replicateID}.txt
|
| |
|
| Submission date |
Aug 20, 2018 |
| Last update date |
Mar 28, 2019 |
| Contact name |
Eric R Reed |
| E-mail(s) |
[email protected]
|
| Organization name |
Tufts University
|
| Department |
Data Intensive Studies Center
|
| Street address |
419 Boston Ave.
|
| City |
Medford |
| State/province |
MA |
| ZIP/Postal code |
02155 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE118797 |
Assessment of a highly multiplexed RNA sequencing platform and comparison to existing high-throughput gene expression profiling techniques [SFL] |
|
| Relations |
| BioSample |
SAMN09865584 |
| SRA |
SRX4579780 |
