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Sample GSM1517073 Query DataSets for GSM1517073
Status Public on Mar 01, 2016
Title RNA-seq, shControl, TGF-beta treated
Sample type SRA
Source name A549
Organism Homo sapiens
Characteristics cell line: A549
shRNA: Negative control
rip: no
tgf-beta treatment: no
histology: lung adenocarcinoma
Treatment protocol For RNA-seq, shRNAs were introduced into cells using lentiviral vectors. Cells were stimulated with 2.5 ng/ml TGF-beta or left untreated for 24 h before harvest. For RIP-seq, A549 cells were cultured in 10-cm dish before lysis.
Growth protocol A549 cells were maintained in Dulbecco's modified Eagle's medium (DMEM #11965; Thermo Scientific) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin G, and 100 µg/ml streptomycin. Cells were grown in a humidified atmosphere with 5% CO2 at 37°C.
Extracted molecule polyA RNA
Extraction protocol For RNA-seq, total RNAs were extracted as described previously (Arase et al., 2014, Cancer Sci). RIP samples were obtained from A549 cells following the manufacturer's protocol (Magna RIP RNA-Binding Protein Immunoprecipitation Kit (Millipore)).
For RNA-seq, Libraries were prepared using Dynabeads mRNA DIRECT Purification Kit (Life Technologies) and Ion Total RNA-seq kit v2 (Thermo Scientific). For RIP-seq, Ion Total RNA-seq kit v2 (Thermo Scientific) was used. Sequencing was performed using Ion PI Chip Kit v2, PI Template OT2 200 Kit v3 and Ion PI Sequencing 200 Kit v3 (Thermo Scientific).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Description control shRNA is stably expressed, TGF-beta treated
Data processing Reads were processed by Tophat2 (version 2.0.10) and Bowtie2 (version 2.1.0) using hg19 version of index files. Parameters used are as follows: -a 6 --segment-length 25 --no-coverage-search --read-realign-edit-dist 0 -G.
FPKM calculation was performed by using Cuffdiff (cufflinks version 2.1.1, with options -m 200 -u).
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-seq, expression data of the four samples were summarized into single processed file by Cuffdiff and are in RNA-seq.genes.fpkm_tracking.txt. For RIP-seq, calculated FPKM values of immunoprecipitated RNA of the four samples were summarized into single processed file by Cuffdiff and are in RIP-seq.genes.fpkm_tracking.txt.
Submission date Sep 30, 2014
Last update date May 15, 2019
Contact name Daizo Koinuma
Organization name University of Tokyo
Department Pathology
Street address Hongo 7-3-1, Bunkyo-ku
City Tokyo
ZIP/Postal code 113-0033
Country Japan
Platform ID GPL17303
Series (1)
GSE61910 Reduced expression of RBM47 enhances Nrf2 activity to promote tumor growth in A549 lung adenocarcinoma cells
BioSample SAMN03084955
SRA SRX717653

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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