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Sample GSM595540 Query DataSets for GSM595540
Status Public on Oct 20, 2010
Title S2_GFP-1
Sample type SRA
 
Source name S2 cell culture, GFP dsRNA
Organism Drosophila melanogaster
Characteristics cell line: S2
treatment: GFP dsRNA
treatment time: 6 days
Treatment protocol S2 cells were treated with dsRNAs (15ug/ml) corresponding to either GFP, eF4AIII or MAGO for six days.
Growth protocol S2 cells were grown in Schneider Medium (Invitrogen) with 10% FBS and with Pen/Strep at 18C degrees.
Extracted molecule total RNA
Extraction protocol Total RNA from S2 cells subjected to treatment with eIF4AIII, mago and GFP dsRNA in duplicate was prepared using TRIzol reagent (Invitrogen). Poly(A)+ mRNAs were enriched using oligo(dT) selection with the Oligotex mRNA Midi kit (Qiagen). The resulting mRNA was then depleted of rRNA molecules using the Ribominus Eukaryote kit (Invitrogen). High-throughput sequencing libraries were prepared according to the SOLiD whole transcriptome library preparation protocol (Applied Biosystems).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model AB SOLiD System 3.0
 
Description Transcriptome of S2 cells treated with a control GFP dsRNA; replicate 1.
Data processing Reads were mapped using ABI Bioscope 1.0.1 to both the Drosophila melanogaster genome (UCSC dm6) and a set of filter sequences, comprised of ribosomal and transfer RNA and sequencing adapters. Filtered reads are not removed from the results but simply marked as such. Both .bam and .wig files were generated using the Whole Transcriptome pipeline described in the ABI documentation. A read was considered unique even if other matches existed of length 3 less than the best match (clear zone = 3). The .wig file was generated using the default values for the sam2wig run (alignment score of 24 or higher and minimum coverage of 10).
 
Submission date Sep 18, 2010
Last update date May 15, 2019
Contact name Hugo Lavoie
E-mail(s) hugo.lavoie@nrc-cnrc.gc.ca
Phone 514-496-6154
Fax 514-496-6213
Organization name CNRC-IRB
Department Genetics
Street address 6100 Royalmount
City Montreal
State/province Quebec
ZIP/Postal code H4P 2R2
Country Canada
 
Platform ID GPL10942
Series (1)
GSE24012 Transcriptional profiling of EJC depletion by RNA-Seq using the SOLiD platform (Applied Biosystems)
Relations
SRA SRX035188
BioSample SAMN00188794

Supplementary file Size Download File type/resource
GSM595540_Droso2_27avril2010_1_GFP1_F3-F1796.bam 3.4 Gb (ftp)(http) BAM
GSM595540_Droso2_GFP1.wig.gz 38.9 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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