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Sample GSM796340 Query DataSets for GSM796340
Status Public on Dec 22, 2011
Title Control RNA-Seq rep2
Sample type SRA
 
Source name Schneider's Drosophila Line 2
Organism Drosophila melanogaster
Characteristics cell type: S2; Schneider's Drosophila Line 2; Marco Blanchette's Lab
cell line: S2
knockdown: control
Treatment protocol Drosophila RNAi was performed by feeding S2 cells with dsRNA prepared with the Megascript T7 dsRNA synthesis kit from Ambion (catalog #1626.) Cells at a density of 2e6 cells/ml were serum starved treated with 10 µg of dsRNA. Additional boosts of 10 µg dsRNA were added at 48 and 96 hours. Cells were harvested at 120 hours.
Growth protocol S2 cells were grown in Schneider's media with 10% FBS at room temperature.
Extracted molecule total RNA
Extraction protocol Two micrograms of DNase-treated total RNA was depleted of Ribosomal RNA with the Ribo-Zero kit from Epicentre (catalog #RZH1046), followed by use of the TruSeq RNA Sample Prep Kit (catalog #FC-122-1001) following manufacturer instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description RNAseq after non-targeting-RNAi; Replicate 2
Data processing RNA-seq analysis was done using TopHat v1.2.0 and Bowtie v0.12.7. Only uniquely mapping reads were used. Fly transcript annotations were from Ensembl 62. Differentially expressed genes after RNAi were called with an adjusted p-value < 0.001 and MA plots were determined by DEseq, v1.4.1. In order to avoid off-target RNAi, independent RNAi experiments, using two different dsRNA regions for each target, were treated as biological replicates for analysis of differential expression.
 
Submission date Sep 14, 2011
Last update date May 15, 2019
Contact name Alexander (Garrett) Garruss
E-mail(s) asg@stowers.org
Organization name Stowers Institute for Medical Research
Lab Shilatifard
Street address 1000 East 50th Street
City Kansas CIty
State/province Missouri
ZIP/Postal code 64110
Country USA
 
Platform ID GPL11203
Series (1)
GSE32120 The little elongation complex (LEC) regulates small nuclear RNA transcription
Relations
Reanalyzed by GSM3274838
SRA SRX097627
BioSample SAMN00718952

Supplementary file Size Download File type/resource
GSM796340_input_rep2.bed.gz 250.5 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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