NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2152526 Query DataSets for GSM2152526
Status Public on Jun 24, 2016
Title RWPE1 - Control Vector, CAD1
Sample type SRA
 
Source name RWPE1, control vector
Organism Homo sapiens
Characteristics cell line: RWPE1
expression: Control vector
Treatment protocol Human RWPE1 cells were engineered with empty vector (altered pTRIPZ), NKX3.1 wild type over-expression, and NKX3.1 (T164A) mutant over-expression. Cells were snap frozen for subsequent molecular analysis.
Growth protocol NA
Extracted molecule total RNA
Extraction protocol RNA was extracted using the MagMAX-96 RNA isolation kit (Ambion). Quality control was performed with Agilent Bioanalyser 2100. We used poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required).
Library preparation was performed using the Illumina TruSeq RNA prep kit. Libraries were sequenced using Illumina HiSeq 2000 at Columbia Genome Center.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description CAD1
Processed data file: RNAseq_human_RWPE1.txt
Data processing Libraries were sequenced using Illumina HiSeq 2000 at Columbia Genome Center. We multiplexed samples in each lane, which yielded targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.
We used RTA (Illumina) for base calling and CASAVA (version 1.8.2) for converting BCL to fastq format, coupled with adaptor trimming. We mapped the reads to a reference genome (Human: NCBI/build37.2) using TopHat (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, TopHat infers novel exon-exon junctions ab initio, and combines them with junctions from known mRNA sequences (refgenes) as the reference annotation. We estimated the relative abundance (aka expression level) of genes and splice isoforms using Cufflinks (version 2.0.2) with default settings. We tested for differentially expressed genes under various conditions using DESeq. It is an R package based on a negative binomial distribution that models the number of reads from RNA-seq experiments and tests for differential expression.
Raw RNA-seq counts were normalized (variance stabilization) using DESeq package in R-studio Version 0.99.484.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text file includes DESeq normalized values for each Sample.
 
Submission date May 13, 2016
Last update date May 15, 2019
Contact name Antonina Mitrofanova
E-mail(s) mitrofanova.antonina@hotmail.com
Organization name Rutgers University
Street address 65 Bergen Street, Rm 923B
City Newark
State/province NJ
ZIP/Postal code 07107
Country USA
 
Platform ID GPL11154
Series (2)
GSE81439 Identification of an NKX3.1-G9a-UTY regulatory network that controls prostate differentiation (Human_RWPE1_RNA-Seq)
GSE81440 Identification of an NKX3.1-G9a-UTY regulatory network that controls prostate differentiation
Relations
BioSample SAMN04999845
SRA SRX1761105

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data is available on Series record

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