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Sample GSM2098471 Query DataSets for GSM2098471
Status Public on Sep 23, 2016
Title PAX8-KO SKOV-3 rep1
Sample type SRA
Source name ovarian cancer cells
Organism Homo sapiens
Characteristics cell type: Human ovarian adenocarcinoma
cell line: SKOV-3
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
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
BioSample SAMN04578262
SRA SRX1659800

Supplementary file Size Download File type/resource
GSM2098471_2_cufflinks_genes.txt.gz 809.3 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

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