|
| Status |
Public on Aug 01, 2015 |
| Title |
RNA-seq, si Arkadia |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
sirna: Arkadia
tgf-beta treatment: no
treatment: Arkadia siRNA transfected
cell line: HEK293T
histology: embryonic kidney cells
|
| 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 |
HEK293T cells were maintained in Dulbecco's modified Eagle's medium (#11965; Life Technologies) supplemented with 10% fetal bovine serum.
|
| 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, 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 |
Arkadia 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 |
Aug 20, 2014 |
| 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) |
| GSE60559 |
RNA-sequencing in HEK293T cells under the knockdown of Arkadia or ESRP2 |
|
| Relations |
| BioSample |
SAMN02999574 |
| SRA |
SRX683754 |
