|
| Status |
Public on Jun 01, 2019 |
| Title |
siCtrl_mRNAseq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
developmental stage: embryonic
tissue: kidney
sirna transfection: Silencer Negative Control No. 2 siRNA, ThermoFisher Cat#AM4613
|
| Treatment protocol |
siRNA transfections were performed using Invitrogen RNAiMAX reverse transfection protocol. Cells were plated in antibiotic free 10% FBS DMEM containing indicated Ambion/ThermoFisher Silencer Select siRNA for a final concentration of 10nM that was pre-incubated in lipofectamine RNAiMAX reagent in Opti-MEM.
|
| Growth protocol |
HEK293 (human embryonic kidney cell line) were maintained at 37°C in a 5% CO2 incubator in Dulbecco’s Modified Eagle Medium (DMEM) with 10% fetal bovine serum.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
1X10^6 HEK293 were transfected with indicated siRNAs for 4, 8, or 16 days. RNA was isolated using QIAGEN RNeasy Plus Mini Kit. Eluted RNA was treated with Ambion DNA-free™ DNA Removal Kit and then Ambion TRIzol reagent, precipitated with isopropanol, and dissolved in sterile water. RNA concentration was measured with a Qubit fluorometer.
One microgram of RNA was fragmented and copied into DNA then PCR amplified with bar-coded primers for separate samples to prepare sequencing libraries using the Illumina TruSeq RNA Sample Preparation procedure.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Sequences were aligned to the hg19 human genome sequence using TopHat v2.
FPKM (fragments per kb per million mapped reads) for each annotated hg19 RefSeq gene ID was determined using Cuffdiff v2 from Cufflinks RNA-Seq analysis tools at http://cufflinks.cbcb.umd.edu.
Bedgraph files were generated using bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig. Cuffdiff output on the series record.
|
| |
|
| Submission date |
Apr 22, 2019 |
| Last update date |
Jun 02, 2019 |
| Contact name |
Bing Ren |
| E-mail(s) |
biren@health.ucsd.edu
|
| Organization name |
UCSD
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE130136 |
De-differentiation by Adenovirus E1A Due to Inactivation of Hippo Pathway Effectors YAP and TAZ [RNA-seq] |
| GSE130137 |
De-differentiation by Adenovirus E1A Due to Inactivation of Hippo Pathway Effectors YAP and TAZ |
|
| Relations |
| BioSample |
SAMN11476249 |
| SRA |
SRX5718128 |
