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Series GSE49587 Query DataSets for GSE49587
Status Public on Aug 07, 2013
Title Developmental arrest of Drosophila survival motor neuron (Smn) mutants accounts for differences in expression of minor intron-containing genes
Organism Drosophila melanogaster
Experiment type Expression profiling by high throughput sequencing
Third-party reanalysis
Summary RNA-seq was used to analyze mRNA levels and splicing differences between wild-type (Oregon R) and Smn null mutant larvae.
 
Overall design Illumina RNA-seq of Oregon R and Smn mutant age-matched larvae from RNA extracted on day four post egg laying.

Conclusions from this study used the publicly available modENCODE data from Graveley et al. Nature 2011 (in addition to our RNA-seq data). We downloaded their SRA files, dumped them to fastq files, and put them through our same analysis pipelines. The renalysis data and details are provided in 'reanalysis.tar' and readme_reanalysis.txt.

The Cufflinks processed file outputs (22 files in 'Cufflinks_outputs.tar') are derived from all of our raw sample files and all of the developmental data mentioned in the readme.txt file. The file format and content description is provided in the 'readme_for_Cufflinks.txt'

Unlike Cufflinks cuffdiff analysis that merged our data with the developmental data, the MISO and DEXSeq analysis was carried out in parallel with analysis of our samples. This generated two additional files for the DEXSeq developmental analysis (DEXSeq output; paired end developmental Graveley et al. Nature 2011):
L2_L3P1_2_DEUtable.txt
L312hr_L3P1_2_DEUtable.txt
Please note that MISO lacks the capacity to incorporate replicates, which contributed to the abundance of these file types.

MISO output file names are prepended with the respective sample/raw data names. For example, EG003_EG007.*miso_bf.txt.gz are MISO comparison of Ore-R R1 (EG003) and Smn R1 (EG007).
 
Contributor(s) Matera AG, Garcia EL
Citation(s) 24006466, 27268418, 35920767, 38664795
Submission date Aug 06, 2013
Last update date May 10, 2024
Contact name Eric L Garcia
E-mail(s) elgarcia@med.unc.edu
Organization name University of North Carolina at Chapel Hill
Department Lineberger Comprehensive Cancer Center
Lab Greg Matera
Street address 3344 Genome Science Bldg
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
 
Platforms (1)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
Samples (4)
GSM1202292 EG003_wild type RNA-seq R1
GSM1202293 EG004_wild-type RNA-seq R2
GSM1202294 EG007_Smn mutant RNA-seq R1
Relations
BioProject PRJNA214351
SRA SRP028543

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE49587_Cufflinks_outputs.tar.gz 152.1 Mb (ftp)(http) TAR
GSE49587_EG003_EG007.a3ss.miso_bf.txt.gz 33.2 Kb (ftp)(http) TXT
GSE49587_EG003_EG007.a5ss.miso_bf.txt.gz 290.1 Kb (ftp)(http) TXT
GSE49587_EG003_EG007.mxe.miso_bf.txt.gz 9.2 Kb (ftp)(http) TXT
GSE49587_EG003_EG007.ri.miso_bf.txt.gz 1.9 Mb (ftp)(http) TXT
GSE49587_EG003_EG007.se.miso_bf.txt.gz 189.0 Kb (ftp)(http) TXT
GSE49587_EG003_EG008.a3ss.miso_bf.txt.gz 33.4 Kb (ftp)(http) TXT
GSE49587_EG003_EG008.a5ss.miso_bf.txt.gz 290.2 Kb (ftp)(http) TXT
GSE49587_EG003_EG008.mxe.miso_bf.txt.gz 9.1 Kb (ftp)(http) TXT
GSE49587_EG003_EG008.ri.miso_bf.txt.gz 1.9 Mb (ftp)(http) TXT
GSE49587_EG003_EG008.se.miso_bf.txt.gz 189.2 Kb (ftp)(http) TXT
GSE49587_EG004_EG007.a3ss.miso_bf.txt.gz 32.5 Kb (ftp)(http) TXT
GSE49587_EG004_EG007.a5ss.miso_bf.txt.gz 274.6 Kb (ftp)(http) TXT
GSE49587_EG004_EG007.mxe.miso_bf.txt.gz 8.6 Kb (ftp)(http) TXT
GSE49587_EG004_EG007.ri.miso_bf.txt.gz 1.8 Mb (ftp)(http) TXT
GSE49587_EG004_EG007.se.miso_bf.txt.gz 179.5 Kb (ftp)(http) TXT
GSE49587_EG004_EG008.a3ss.miso_bf.txt.gz 32.8 Kb (ftp)(http) TXT
GSE49587_EG004_EG008.a5ss.miso_bf.txt.gz 275.2 Kb (ftp)(http) TXT
GSE49587_EG004_EG008.mxe.miso_bf.txt.gz 8.5 Kb (ftp)(http) TXT
GSE49587_EG004_EG008.ri.miso_bf.txt.gz 1.8 Mb (ftp)(http) TXT
GSE49587_EG004_EG008.se.miso_bf.txt.gz 179.4 Kb (ftp)(http) TXT
GSE49587_L2_L3P1_2_DEUtable.txt.gz 2.4 Mb (ftp)(http) TXT
GSE49587_L312hr_L3P1_2_DEUtable.txt.gz 2.3 Mb (ftp)(http) TXT
GSE49587_ORvSmn_DEUtable.txt.gz 2.8 Mb (ftp)(http) TXT
GSE49587_RAW.tar 333.5 Mb (http)(custom) TAR (of BEDGRAPH)
GSE49587_readme.txt 4.6 Kb (ftp)(http) TXT
GSE49587_readme_for_Cufflinks.txt 3.0 Kb (ftp)(http) TXT
GSE49587_readme_for_reanalysis.txt 8.2 Kb (ftp)(http) TXT
GSE49587_reanalysis.tar.gz 16.7 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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