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Sample GSM4233002 Query DataSets for GSM4233002
Status Public on Dec 27, 2019
Title A549_IL1b_21d_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 21
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 SAMN13683189
SRA SRX7442869

Supplementary file Size Download File type/resource
GSM4233002_Sample_S6.count.txt.gz 212.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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