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Sample GSM900512 Query DataSets for GSM900512
Status Public on May 01, 2012
Title Caf40 knockdown testis expression profiling 2
Sample type SRA
 
Source name Caf40 testis knockdown
Organism Drosophila melanogaster
Characteristics developmental stage: 1-7d adult
strain: Oregon-R
genotype/variation: nosGal4>>UAS-Caf40-RNAi
tissue: dissected testis
Treatment protocol NA
Growth protocol standard cornmeal
Extracted molecule total RNA
Extraction protocol standard Illumina single-end mRNA-seq library prep Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer
 
Description Trizol-chloroform-Qiagen
Data processing The sequences in fastq files were mapped back to whole genome sequences using Bowtie, allowing 2 mismatches; all the unmapped sequences were then mapped to all possbile exon-exon conjuction sequences as annotated by flybase using Bowtie, allowing 2 mismatches. The number of reads of a gene is then calculated as the total number of unique sequence read overlapping with annotated exonic regions of the gene and RPKM values are calculated as the number of reads per kilo base of annotated exon length per million total uniquely mapped reads.
Genome Build:
nos_Caf40_RNAi_2_testis_RPKM_value.txt: dm3
 
Submission date Mar 23, 2012
Last update date May 15, 2019
Contact name Sidi Chen
E-mail(s) chensidi@mit.edu
Phone 7734144158
Organization name MIT
Department Biology
Lab Sharp
Street address 77 Mass Ave, 76-461
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platform ID GPL9058
Series (2)
GSE36764 Expression profiling of Drosophila testes
GSE36920 Reshaping of global gene expression networks and sex-biased gene expression by integration of a nascent gene
Relations
Reanalyzed by GSM3277409
SRA SRX142030
BioSample SAMN00855349

Supplementary file Size Download File type/resource
GSM900512_nos_Caf40_RNAi_2_testis_RPKM_value.txt.gz 268.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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