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Status |
Public on Aug 01, 2015 |
Title |
RNA-seq, si ESRP2 OS-RC-2 |
Sample type |
SRA |
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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
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Treatment protocol |
siRNAs were introduced into cells using Lipofectamine RNAiMAX reagent (Invitrogen) with a reverse method. Cells were harvested 48 h after seeding.
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Ion Torrent Proton |
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Description |
ESRP2 siRNA transfected genes.fpkm_tracking.txt isoforms.fpkm_tracking.txt
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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.
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Submission date |
Mar 10, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Daizo Koinuma |
E-mail(s) |
d-koinuma@umin.ac.jp
|
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 |
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Relations |
BioSample |
SAMN03397423 |
SRA |
SRX950716 |