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Sample GSM1210537 Query DataSets for GSM1210537
Status Public on Aug 17, 2013
Title D. melanogaster RNA-seq
Sample type SRA
 
Source name Whole animal
Organism Drosophila yakuba
Characteristics developmental stage: White prepupa
organism: Drosophila yakuba
Extracted molecule total RNA
Extraction protocol RNA was isolated with Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer
 
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence (using fastx_clipper -a GATCGGAAGAGC -M 12 -Q 33), then mapped to the appropriate whole genome using tophat (tophat -o dmel_WPP --solexa1.3-quals -p 8 --bowtie1 -n 2 -g 1 -M -G dmel.gtf).
Duplicated reads were removed with SAMtools rmdup command (with -s flag for single-end data).
FPKMs for each gene were calculated using the cufflinks software (cufflinks -b -u).
Genome_build: dm3 (D. melanogaster), droSim1 (D. simulans), droYak2 (D. yakuba), dp4 (D. pseudoobscura)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample. Format is cufflinks standard.
 
Submission date Aug 16, 2013
Last update date May 15, 2019
Contact name Kevin White
Organization name University of Chicago
Department Institute for Genomics and Systems Biology
Lab Kevin White lab
Street address 900 E. 57th St. Room 10100
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platform ID GPL11000
Series (1)
GSE49945 Genome-wide comparative ChIP-seq data of H3K27me3 and RNA-seq data in Drosophila white prepupa on Illumina Genome Analyzer
Relations
BioSample SAMN02318562
SRA SRX336060

Supplementary file Size Download File type/resource
GSM1210537_dmel_WPP.fpkm.txt.gz 413.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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