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| Status |
Public on Jan 15, 2019 |
| Title |
SSX-flagIP 1 |
| Sample type |
SRA |
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| Source name |
transfected SL2 cells
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| 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
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| 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
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| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| 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
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| Submission date |
Apr 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Gerhard Lehmann |
| E-mail(s) |
gerhard.lehmann@vkl.uni-regensburg.de
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| Organization name |
University of Regensburg
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| Department |
Biochemistry 1
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| Street address |
Universitaetsstrasse 31
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| City |
Regensburg |
| ZIP/Postal code |
93053 |
| Country |
Germany |
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| 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 |
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| Relations |
| BioSample |
SAMN06830480 |
| SRA |
SRX2764521 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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