|
| Status |
Public on May 10, 2013 |
| Title |
ribosomal RNA-depleted total RNA wt OSCs - rep2 |
| Sample type |
SRA |
| |
|
| Source name |
ribosomal RNA-depleted total RNA wt OSCs
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Ovarian Somatic Cells (OSC)
genotype: wild-type
Stage: -
|
| Growth protocol |
OSC were grown at 27 degrees on M3 medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was isolated with Trizol
mRNA from wildtype OSCs was selected with Dynabeads Oligo(dT) (Invitrogen) from total RNA, fragmented and reverse transcribed with random hexamers. Strand-specific libraries were prepared using the UDG-digestion-based strategy and cloned with NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (NEB)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0)
N-containing reads were discarded
reads were trimmed to high-quality bases 6-50 using HomerTools, version 3.9 and mapped to genome and transcriptome using in-house developed pipeline
Reads were mapped to the dm3 genome (Release 5) and transcriptome using bowtie (bowtie -f -v 3 -m 1 --best --strata --quiet -S INDEX -) and bfast reconciling the outputs. We estimated RPKM values for each gene based on the number of reads falling over each exon merging exons from a all genes' isoforms into one meta-transcript. Reads counts were normalized by the total reads per library and the merged meta-gene exons lengths.
Genome_build: Release 5 (dm3)
|
| |
|
| Submission date |
Apr 09, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Dominik Handler |
| E-mail(s) |
[email protected]
|
| Organization name |
IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences
|
| Lab |
Brennecke
|
| Street address |
Dr. Bohr-Gasse 3
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE45894 |
The genetic framework of the Drosophila piRNA pathway |
|
| Relations |
| Reanalyzed by |
GSM3282996 |
| SRA |
SRX262874 |
| BioSample |
SAMN02010576 |
