|
| Status |
Public on Aug 07, 2013 |
| Title |
EG008_Smn mutant RNA-seq R2 |
| Sample type |
SRA |
| |
|
| Source name |
Smn mutant RNA-seq
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: SmnX7/D
age: 74 ± 2 hours post egg laying
tissue: whole larvae
|
| Growth protocol |
Larvae were cultured on molasses and agar at room temperature (24 ± 1°C)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Larvae were collected and washed with water at 74 ± 2 hours post egg laying. Larvae were then crushed in TRIzol and stored at -80°C.
Illumina TruSeq RNA sample preparation kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: ORvSmn_DEUtable.txt
EG004_EG008.a3ss.miso_bf.txt.gz
EG004_EG008.a5ss.miso_bf.txt.gz
EG004_EG008.mxe.miso_bf.txt.gz
EG004_EG008.ri.miso_bf.txt.gz
EG004_EG008.se.miso_bf.txt.gz
EG003_EG008.a3ss.miso_bf.txt.gz
EG003_EG008.a5ss.miso_bf.txt.gz
EG003_EG008.mxe.miso_bf.txt.gz
EG003_EG008.ri.miso_bf.txt.gz
EG003_EG008.se.miso_bf.txt.gz
|
| Data processing |
base-calling: CASAVA v.1.8.2
alignment: TopHat v2.0.8 with Bowtie v2.1.0 and Samtools v0.1.19
analysis of differential expression: Cufflinks v2.0.2
analysis of splicing differences: DEXSeq v1.0.2
analysis of splicing differences: MISO v0.4.8
Genome_build: dm3
Supplementary_files_format_and_content: tracking and diff files, Cuffdiff output; different exon id file, DEXSeq output; pairwise comparison of alternative splicing events file, MISO output; bedGraph files, converted from Tophat output bam files
|
| |
|
| Submission date |
Aug 06, 2013 |
| Last update date |
May 15, 2019 |
| 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 |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE49587 |
Developmental arrest of Drosophila survival motor neuron (Smn) mutants accounts for differences in expression of minor intron-containing genes |
|
| Relations |
| Reanalyzed by |
GSM3284459 |
| BioSample |
SAMN02303470 |
| SRA |
SRX331969 |
