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Sample GSM2585515 Query DataSets for GSM2585515
Status Public on Nov 20, 2017
Title Drosophila pseudoobscura male body small RNA [V112_dpse_male_body]
Sample type SRA
Source name D. pseudoobscura male body small RNA
Organism Drosophila pseudoobscura
Characteristics tissue: abdomen and thorax
Extracted molecule total RNA
Extraction protocol Male and female bodies were isolated in bulk using sieves after sorting by sex. Animals were flash frozen in liquid nitrogen followed by vortexing. This procedure severs heads from the thorax and abdomen allowing separation of these two body parts when sifted through chilled fine mesh sieves. Here we used a .600mm sieve to collect male bodies. Total RNA was then extracted from the bodies using TRIzol according to manufacturer protocol.
For Illumina GAII Libraries: From total RNA, ~18-26 nt fraction was isolated using PAGE and cloned using ligation to adapters requiring 5' monophosphate and 3' OH.
For Illumina HiSeq Library: Libraries were created with the Illumina truseq small RNA cloning kit using a modified protocol. Small RNAs in the 18-29nt size range were first isolated from total RNA by PAGE purification before cloning. PAGE purification was also performed after ligation of RNAs to 3’ and 5’ linkers before processing in subsequent steps. All enzymatic reactions and oligos were used as indicated by manufacturer.
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer II
Description male bodies
Data processing 3' adapter sequences were trimmmed using the fastx_clipper utility
reads < 15nt in size were filtered
identical read sequences were collapsed using the fastq_collapser utility
Supplementary_files_format_and_content: read count table files (columns are read read sequence and number of reads)
Submission date Apr 20, 2017
Last update date May 15, 2019
Contact name Jaaved Mohammed
Organization name Stanford University
Department Chemical and Systems Biology
Lab Joanna Wysocka
Street address 265 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platform ID GPL9958
Series (1)
GSE98013 Small RNAs from 11 Drosophila species
BioSample SAMN06770074
SRA SRX2749093

Supplementary file Size Download File type/resource
GSM2585515_V112_readCountTable.txt.gz 10.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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