|
| Status |
Public on Jan 19, 2015 |
| Title |
r2d2_het_ovary |
| Sample type |
SRA |
| |
|
| Source name |
ovary
|
| Organism |
Drosophila melanogaster |
| Characteristics |
chemical treatment of isolated rna: none
tissue: ovary
genotype: r2d2 heterozygous mutant
|
| Treatment protocol |
no special treatment was performed on the live animals
|
| Growth protocol |
flies were reared on standard yeast / cornmeal / molasses medium and harvested 5 days after eclosion.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The dissected body parts (head&thorax vs. ovaries) were ground in Trizol with a micro-pestle, then phase separation and precipitation was perfomed according to the manufacturer's instructions.
Total RNA was isolated using Trizol and size-selected on polyacrylamide/urea gels [~18-30 nt). In a first ligation step, pre-adenylated 3'-linkers were ligated to the 3'-end of the small RNAs (AMP-5'p=5'pCTGTAGGCACCATCAATdideoxyC-3') in the absence of ATP. After gel-purification of the ligation products, a 5'-Adapter was ligated in the presence of ATP 5('-rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrC rUrCrUrUrCrCrGrArUrCrU-3'). Following reverse transcription with 5'-ATTGATGGTGCCTACAG-3', PCR was performed to append Adapter sequences for Illumina sequencing as well as indexes for multiplexing. A constant 5'-primer (5'-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACG-3') was combined with one of four 3'-index primers (5'-CAAGCAGAAGACGGCATACGAGGATCCGATTGATGGTGCCTACAG-3', 5'-CAAGCAGAAGACGGCATACGACAGCTGGATTGATGGTGCCTACAG-3', 5'-CAAGCAGAAGACGGCATACGATCTAGAGATTGATGGTGCCTACAG-3', 5'-CAAGCAGAAGACGGCATACgaATCGATGATTGATGGTGCCTACAG-3'). Sequencing was single-end (75 nt length), 3'-adapters and indexes were sequenced together with the small RNAs.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Reads were first sorted according to their sample index, then the 3'-adapter sequence and everything else 3'-of it was removed.
Reads were sorted into unique sequences with sequence counts
Reads were size-selected for 21-23 nt or 24-29-30 nt length .
Genome_build: n.a.
Supplementary_files_format_and_content: is a text file with the read sequence and the number of occurrences.
|
| |
|
| Submission date |
Mar 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Klaus Förstemann |
| E-mail(s) |
foerstemann@lmb.uni-muenchen.de
|
| Organization name |
Ludwig-Maximilians University
|
| Department |
Gene Center
|
| Lab |
Förstemann
|
| Street address |
Feodor-Lynen 25
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11203 |
| Series (1) |
| GSE45290 |
Transposon defense by endo-siRNAs, piRNAs and somatic pilRNAs: Roles of Loqs-PD and R2D2 |
|
| Relations |
| SRA |
SRX252207 |
| BioSample |
SAMN01984518 |
