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Sample GSM876117 Query DataSets for GSM876117
Status Public on Dec 01, 2013
Title Lu003
Sample type SRA
Source name VFP-SmD3_Ctrl
Organism Drosophila melanogaster
Characteristics strain: nos Gal4 VFP-SmD3
tissue: ovary
rip antibody: none
Growth protocol Oregon Red or transgenic newly-eclosed fruitflies were grown on corn syrup solids with yeast for 2~4 days before ovary dissection.
Extracted molecule total RNA
Extraction protocol Lysates were clarified from dissected Drosophila ovaries and RNA-Sm protein complexes were isolated with antibody. RNA was purified from the immunoprecipitate, reverse transcribed and made into doublestranded DNA. Libraries were prepared according to Illumina's instructions. Briefly, DNA was fragmented, ligated to adapters and PCR amplified with Illumina primers for 15 cycles. The resultant DNA was purified from an agarose gel and captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
Data processing A custom D. melanogaster expanded genome was made using the Drosophila genome (dm3, April 2006) and gene annotations. Filtered sequence reads (chastity >=0.6) were mapped to the expanded genome using Bowtie, allowing up to 2 mismatches and 10 mapped locations. Bowtie-mapped files were then analyzed using the ERANGE software to count the number of unique, spliced and multiple reads, and reads that mapped to putative new genes, measured as RPKM (reads per kb per million reads) values.
To create the wiggle files, sequence files were mapped to D. melanogaster expanded genome and output as sam files, and then converted to UCSC track files using samtools and BEDtools.
Genome Build: dm3
Lu003.newregions.txt: dm3
Lu003.wig: dm3
Submission date Feb 15, 2012
Last update date May 15, 2019
Contact name Zhipeng Lu
Organization name Stanford University
Department Department of Dermatology
Lab Howard Chang
Street address 269 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platform ID GPL9061
Series (1)
GSE35842 RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins
Reanalyzed by GSM3276602
SRA SRX120122
BioSample SAMN00790468

Supplementary file Size Download File type/resource 293.4 Kb (ftp)(http) RPKM
GSM876117_Lu003.newregions.txt.gz 479 b (ftp)(http) TXT
GSM876117_Lu003.wig.gz 11.1 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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