GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1631245 Query DataSets for GSM1631245
Status Public on Aug 01, 2015
Title RNA-seq, si ESRP2 OS-RC-2
Sample type SRA
Source name OS-RC-2
Organism Homo sapiens
Characteristics sirna: ESRP2
tgf-beta treatment: no
histology: clear-cell renal cell carcinoma
treatment: ESRP2 siRNA transfected
cell line: OS-RC-2
Treatment protocol siRNAs were introduced into cells using Lipofectamine RNAiMAX reagent (Invitrogen) with a reverse method. Cells were harvested 48 h after seeding.
Growth protocol OS-RC-2 cells were obtained from RIKEN Cell Bank (Tsukuba, Japan) and maintained in RPMI 1640 (#11875; Life Technologies) supplemented with 10% fetal bovine serum. Cells were grown in a humidified atmosphere with 5% CO2 at 37°C.
Extracted molecule polyA RNA
Extraction protocol Total RNAs were extracted as described previously (Mizutani et al., 2011, J Biol Chem).
Libraries were prepared using Dynabeads mRNA DIRECT Purification Kit (Life Technologies) and Ion Total RNA-seq kit v2 (Thermo Scientific). Sequencing was performed using Ion PI Chip Kit v2 BC and ion PI IC200 kit (Thermo Scientific).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Description ESRP2 siRNA transfected
Data processing RNA-seq reads were trimmed down to 150 bases and 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: Expression data of the three samples were summarized into single processed file by Cuffdiff. Gene-level expressions are in genes.fpkm_tracking.txt and isoform-level expressions are in isoforms.fpkm_tracking.txt.
Submission date Mar 10, 2015
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)
GSE66741 RNA-sequencing in OS-RC-2 cells under the knockdown of Arkadia or ESRP2
BioSample SAMN03397423
SRA SRX950716

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap