|
| Status |
Public on Mar 07, 2014 |
| Title |
Ras-expressing Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Fat body
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: offsprings of Bx Gal4 x UAS-RAS V12
developmental stage: wandering larvae
genotype/variation: Ras-expressing
tissue: fat body
|
| Treatment protocol |
no treatment
|
| Growth protocol |
yeast-potato meal
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction: fat body tissues collected in Trizol (Invitrogen Cat. no.:10296-028), wortex and and freeze at -80C. After thawing the Qiagen RNeasy Mini Kit (Cat. no.: 74104) was used to prepare RNA. Qiagen DNase for DNA degradation and subsequent purification was applied. Multiplex library was constructed for mRNA sequencing using Illumina adaptors and subjected to HiSeq2000 sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 5
|
| Data processing |
Base conversion was done using Illumina’s OLB v1.9.
Reads were mapped to Drosophila_melanogaster.BDGP5.25.64.gtf using Tophat v1.0.14 (Trapnell et al, 2009)
Cufflinks v0.0.5 was used to calculate FPKM values
Cuffcompare and Cuffdiff were used to calculate the differential gene expression between the samples
Cufflinks, Cuffcompare and Cuffdiff were run using Galaxy (https://main.g2.bx.psu.edu/root)
Genome_build: Drosophila_melanogaster.BDGP5.25.64.gtf (Release 5 http://www.ncbi.nlm.nih.gov/assembly/GCF_000001215.2/)
Supplementary_files_format_and_content: The .txt files report gene expression data [output files of Cufflinks].
Supplementary_files_format_and_content: The .xls files report differential gene expression [output files of Cuffdiff]. The .xls files are linked to the Series record as supplementary files.
|
| |
|
| Submission date |
Oct 11, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Ulrich Theopold |
| E-mail(s) |
[email protected]
|
| Phone |
+46-(0)8-164181
|
| Fax |
+46-(0)8- 166488
|
| URL |
http://www.molbio.su.se/
|
| Organization name |
Stockholm University
|
| Department |
Molecular Biology and Functional Genomics
|
| Street address |
Svante Arrhenius Laboratories 20c
|
| City |
Stockholm |
| ZIP/Postal code |
SE-106 91 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE41487 |
Analysis of the humoral immune response against aberrant self by RNA sequencing of the fat body in Drosophila melanogaster |
|
| Relations |
| Reanalyzed by |
GSM3281661 |
| SRA |
SRX193500 |
| BioSample |
SAMN01760914 |
