|
| Status |
Public on Dec 27, 2019 |
| Title |
A549_IL1b_w6d_repA |
| Sample type |
SRA |
| |
|
| Source name |
A549 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: lung
cell type: non-small cell lung cancer
treatment: IL1beta treated
time point: day 6 posttreatment
|
| Growth protocol |
A549 cells were cultured in standard RPMI media with 10% FBS with or without IL-1beta (1ng/ml) for indicated days, and split every 3-4 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted from the cells using the Qiagen RNeasy Mini Kit following the manufactural instruction
Libraries for RNA-Seq were prepared with KAPA Stranded mRNA-Seq Kit. Library preparation performed by Techonology Center for Genomics & Bioinformatics (TCGB) at UCLA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Biological repication 1 of 3
|
| Data processing |
Basecalls, demultiplex and adapter trimming were performed with Illumina Bcl2fastq2 v 2.17
Sequenced reads were mapped to Human Ensemble GRCh37 genome by using tophat2 v.2.0.14 and bowtie2 v.2.2.5 with following parameters -p 4 -g 1 --no-coverage-search.
Gene counts were performed with htseq-count function in HTSeq v.0.6.1. Aligned sequences from tophat2 were sorted by name before subjected to htseq-count analysis with following parameters: -s no -a 10 -m intersection-strict -q
Genome_build: GRCh37 human genome
Supplementary_files_format_and_content: tab-delimited text files include raw feature counts for each sample
|
| |
|
| Submission date |
Dec 26, 2019 |
| Last update date |
Dec 27, 2019 |
| Contact name |
Linh My Tran |
| E-mail(s) |
linhtran@ucla.edu
|
| Organization name |
University of Los Angeles
|
| Department |
Medicine - Pulmonary & Critical Care
|
| Lab |
Dubinett Lab
|
| Street address |
Box 951690, 37-131 CHS
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90095-1690 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE142620 |
Chronic IL-1β-induced inflammation regulates epithelial-to-mesenchymal transition memory phenotypes via epigenetic modifications in non-small cell lung cancer |
|
| Relations |
| BioSample |
SAMN13683187 |
| SRA |
SRX7442871 |
