NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1032807 Query DataSets for GSM1032807
Status Public on Nov 08, 2012
Title Dmel_WPP_RNAseq_3
Sample type SRA
 
Source name Whole animal white prepupa
Organism Drosophila melanogaster
Characteristics developmental stage: white prepupa
Growth protocol The three sequenced inbred fly lines for the different Drosophila species are grown in room temperature on standard fly food. The white prepupa whole animals are collected within 15 min time interval.
Extracted molecule total RNA
Extraction protocol Total RNA samples are isolated using Trizol Chroloform, followed by QIAGEN column purification.
RNA seq libraries are prepared using standard Illumina single end RNA seq library protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer
 
Description Sample 3
Data processing Sequencing data are mapped to the genome as well as the annotated exon-exon conjunctions using Bowtie, allowing 2 mismatches.
Only uniquely mapped reads were used to generate the read counts and RPKM values for each gene following the methods described in Mortazavi et al 2008 Nature Methods paper.
Genome_build: dm3, droSim1, droYak2
Supplementary_files_format_and_content: tab delimited file including read counts and RPKM values for each gene (abundance measurements)
 
Submission date Nov 07, 2012
Last update date May 15, 2019
Contact name Kevin P. White
E-mail(s) kpwhite@uchicago.edu
Organization name University of Chicago
Department Institute for Genomics and Systems Biology
Street address 900 E. 57th STR. 10th FL.
City Chicago
State/province IL
ZIP/Postal code 60615
Country USA
 
Platform ID GPL9058
Series (1)
GSE24449 Genome-wide comparative ChIP-seq data of CTCF and RNA-seq data in Drosophila white prepupa on Illumina Genome Analyzer
Relations
Reanalyzed by GSM3281760
SRA SRX203259
BioSample SAMN01803794

Supplementary file Size Download File type/resource
GSM1032807_dmel_s_8_WPP_RPKM_2.txt.gz 262.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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