NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2098481 Query DataSets for GSM2098481
Status Public on Sep 23, 2016
Title PAX8-KO FT194 rep2
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 Pax8 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 Pax8 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 SAMN04578272
SRA SRX1659810

Supplementary file Size Download File type/resource
GSM2098481_12_cufflinks_genes.txt.gz 820.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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