|
| Status |
Public on Nov 11, 2013 |
| Title |
brat adult heads_replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
female heads
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype/variation: brat mutant
age: 1-3 days
|
| Treatment protocol |
Fly heads were isolated by shaking and sieving in liquid nitrogen
|
| Growth protocol |
Flies heads were maintained and crossed according to standard procedures, and female flies were collected 2-4 days after hatching
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from adult fly heads by TRIzol purification (Invitrogen)
Total RNA(~1µg) was enriched for polyA mRNA (Dynabeads, Invitrogen), 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 IIx |
| |
|
| Data processing |
Basecalling was performed with RTA Version 1.6.32.0
The strand specific paired-end reads were screened for ribosomal RNA by alignment (max. 3 mismatches) against known rRNA sequences (RefSeq) using Bowtie.
The rRNA subtracted paired-end reads were aligned with TopHat (v1.2.0) against the Drosophila melanogaster genome (release 5). Introns of 30–150,000 bp were allowed based on FlyBase statistics. Maximum multihits was set to 1, and microexon-search was enabled. Additionally, a gene model was provided as GTF (Ensembl BDGP5.25.60).
Aligned reads in valid pairs were subjected to FPKM estimation using Cufflinks (v1.0.2). In this step, bias detection and correction was performed. Furthermore, only those fragments compatible with Ensembl annotation (BDGP5.25.60) were allowed and counted towards the number of mapped hits used in the FPKM denominator.
Genome_build: FlyBase dmel_r5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (Standard output cufflinks);
|
| |
|
| Submission date |
Oct 18, 2013 |
| 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 |
GPL11203 |
| Series (1) |
| GSE51412 |
Transcriptome and proteome quantification of a tumor model provides novel insights into post-transcriptional gene regulation |
|
| Relations |
| Reanalyzed by |
GSM3284789 |
| BioSample |
SAMN02377949 |
| SRA |
SRX365381 |
