NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2589039 Query DataSets for GSM2589039
Status Public on Jan 15, 2019
Title SSX-flagIP 2
Sample type SRA
 
Source name transfected SL2 cells
Organism Drosophila melanogaster
Characteristics cell type: male, see Schneider's Drosophila Line 2 [D. Mel. (2), SL2] (ATCC CRL-1963)
tag: FLAG-3xHA-tag
ip-antibody: anti-FLAG M2, mouse monoclonal
Extracted molecule total RNA
Extraction protocol RNA extraction, rRNA depletion
Pico Input SMARTer Stranded Total RNA-Seq Kit (Clontech)
RNA-seq, paired-end 51 nt
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Data processing Illumina HiSeq
Trimming of Pico Input SMARTer Stranded Total RNA-Seq Kit Adapter: Trimmomatic headcrop 3 nt at the 5'-end of the forward read
Adapter clipping with Trimmomatic: ILLUMINACLIP:TruSeq_HT_PE.fa:2:30:15:2:true TRAILING:26 MINLEN:27
Aligment with Tophat2 against Drosophila_melanogaster.BDGP6.30 (Ensembl): option -library-type fr-secondstrand
Reads were summarized per gene using featureCounts (Rsubread, R-Bioconductor), annotation: Drosophila_melanogaster_BDGP6_30.gtf: option strandspecific 1
Differential enrichment of genes bound to Sxl and Ssx vs GFP were analysed using DESeq2 (R-Bioconductor)
Genome_build: ftp://ftp.ensemblgenomes.org/pub/release-30/metazoa/fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.30.dna.genome.fa.gz
Supplementary_files_format_and_content: Excel spreadsheet: DESeq results, significantly upregulated genes
 
Submission date Apr 25, 2017
Last update date May 15, 2019
Contact name Gerhard Lehmann
E-mail(s) gerhard.lehmann@vkl.uni-regensburg.de
Organization name University of Regensburg
Department Biochemistry 1
Street address Universitaetsstrasse 31
City Regensburg
ZIP/Postal code 93053
Country Germany
 
Platform ID GPL13304
Series (2)
GSE98187 Flipping the switch on Sex-lethal expression: Sister of Sex-lethal antagonizes Sxl-dependent alternative splicing to maintain a male-specific gene expression pattern in Drosophila (RIP-Seq)
GSE98189 Flipping the switch on Sex-lethal expression: Sister of Sex-lethal antagonizes Sxl-dependent alternative splicing to maintain a male-specific gene expression pattern in Drosophila
Relations
BioSample SAMN06830479
SRA SRX2764522

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap