|
| Status |
Public on Aug 21, 2012 |
| Title |
wild type neuron 1 (tech. Repl. 1) |
| Sample type |
SRA |
| |
|
| Source name |
wild type neuron
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue source: larval brain
cell type: neuron (differentiated daughter cells)
Stage: late third instar
marker: cells expresses nuclear GFP marker (UAS-stingerGFP)
|
| Growth protocol |
Flies expressing UAS-stingerGFP under asense-Gal4 were flipped on fresh food, left to lay for 24 h, and then kept at 25 degree for another five days, before dissection of larval brains.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Neuroblasts and neurons were FACS sorted, and RNA was isolated using Trizol reagent. Total RNA(~1µg) was enriched for polyA mRNA, fragmented and first strand and second strand (dUTP, instead dTTP was used) was generated. Library preparation was done using a modified protocol from Illumina with NEBNext DNA sample Prep Reagent kits (NEB), and UGDase treatment was done to confer strand specificity.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Sample 6
|
| Data processing |
Basecalls performed using Bustard v1.8.0
The strand specific paired-end reads were screened for ribosomal RNA by aligning with BWA (v0.6.1) against known rRNA sequences (RefSeq). Non matching reads were considerd downstream.
The rRNA subtracted paired-end reads were aligned with TopHat (v1.4.1) against the Drosophila melanogaster genome (FlyBase r5.44) and a maxiumum of 6 missmatches. Introns between 20-150000 bp are allowed which is based on FlyBase statistics. Maximum multihits was set to 1 and InDels as well as Microexon-search was enabled. Additionally, a gene model was provided as GTF (FlyBase r5.44).
Aligned reads in valid pairs are subjected to FPKM estimation with Cufflinks (v1.3.0). In this step bias detection and correction was performed. Furthermore, only those fragments compatible with FlyBase annotation (r5.44) were allowed and counted towards the number of mapped hits used in the FPKM denominator. snRNA, rRNA, tRNA, snoRNA and pseudogenes are masked.
The aligned reads were counted with HTSeq. Counts for technical replicates are summed up. The polyA containing transcripts were subjected to differential expression analysis with DESeq (v1.8.3). DESeq parameters were chosen to match the DESeq publication (Anders S, Huber W., 2010). 'DESeq.nbVsneuron-orig-FDR0.01.txt' data file for differential expression (FDR<0.01) is available on a Serie records.
Genome_build: FlyBase dmel_r5.44
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (Standard output cufflinks); tab-delimited text file with differentially expressed genes for the whole analysis (standard output DESeq).
|
| |
|
| Submission date |
Jun 15, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Rainer Burkard |
| E-mail(s) |
thomas.burkard@imba.oeaw.ac.at
|
| Organization name |
IMBA
|
| Street address |
Dr. Bohrgasse 7
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL9061 |
| Series (1) |
| GSE38764 |
Transcriptome analysis of Drosophila neural stem cells reveals a transcriptional network for self-renewal. |
|
| Relations |
| Reanalyzed by |
GSM3278325 |
| SRA |
SRX154753 |
| BioSample |
SAMN01054453 |
