|
| Status |
Public on Sep 23, 2016 |
| Title |
WT FT-194 rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Fallopian tube epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Immortalized Fallopian tube secretory epithelial cell
cell line: FT-194
sirna: si-RNA Ctr transfected
|
| Treatment protocol |
For RNA interference experiments, SKOV-3 and FT194 cells were transfected in replicate with 5 nM of PAX8 siRNA or Non-Targeting siRNA (Ambion, Life Technologies).
|
| Growth protocol |
The human ovarian carcinoma cell line SKOV-3 was grown in RPMI medium containing 10% fetal bovine serum. The immortalized Fallopian tube secretory epithelial cell line FT194 was maintained in DME-F12 medium containing 2% Ultroser G serum (PALL).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen). For RNA-seq 2μg of total RNA was extracted 24h after transfection.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
si-RNA Ctr transfected
|
| Data processing |
Illumina Configure BCL2FASTQ v1.8.4 software used for basecalling.
Sequenced reads were mapped to hg19/GRCh37 whole genome using Tophat 2.0.12
For each sample, Cufflinks was used to estimate the expression level, expressed as Fragment mapped per kilobase of exons per million mapped reads(FPKM)
Differential expression analyses were performed with Cuffdiff2 and expressed as Fragment mapped per kilobase of exons per million mapped reads(FPKM)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt files include FPKM values for each Sample derived from Cufflink analysis
Supplementary_files_format_and_content: xls files include FPKM values derived from CuffDiff analysis
|
| |
|
| Submission date |
Mar 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Stella Zannini |
| E-mail(s) |
s.zannini@ieos.cnr.it
|
| Organization name |
CNR IEOS
|
| Street address |
Via Pansini 5
|
| City |
Naples |
| ZIP/Postal code |
80131 |
| Country |
Italy |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE79572 |
Candidate genes and pathways downstream of PAX8 involved in ovarian high-grade serous carcinoma |
|
| Relations |
| BioSample |
SAMN04578271 |
| SRA |
SRX1659809 |
