|
| Status |
Public on Nov 12, 2012 |
| Title |
endogenous small RNAs from Dnmt2 mutants; 2 day recovery, 12 day old, male, whole body minus testis |
| Sample type |
SRA |
| |
|
| Source name |
Dnmt2 mutants; 2 day recovery, male, whole body minus testis
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: w1118; Dnmt2 mutant/Dnmt2 mutant;+/+
developmental stage: adult males, 12 days
tissue: whole body without testis
rna fraction: small RNAs (25-70 nucleotides)
|
| Treatment protocol |
Male flies were heat-shocked (37 C for one hour) in a water bath, followed by a recovery period of a) 5 hours at RT or b) 2 days before extracting total RNA
|
| Growth protocol |
Flies were cultured on standard fly food in a humidified incubator (60% humidity) at a 12/12 hour day-night light cycle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Germ line (testes) was separated from carcasses (soma) and RNA was extracted from soma using Trizol. 200 µg of total RNA per experiment were depleted of 2S rRNA using biotinylated DNA-oligos and streptavidin magnetic beads. 25- to 70-nt small RNAs from depleted total RNA were gel extracted from a 15% denaturing acrylimide gel (0.5´ TBE, 0.42 g/ml urea, 15% 19:1 acrylimide:bisacrylimide). After elution from the gel (twice incubated at 4°C in 0.4 M NaCl for 12 hours), RNAs were precipitated using ethanol and further processed for bar-coded RNA sequencing (6 barcodes) using the TrueSeq small RNA sample preparation kit (Illumina). Sequencing of samples was performed on a HighSeq platform (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Linkers and barcode sequences were extracted from the raw tags. Remaining tags were imported into Galaxy (http://main.g2.bx.psu.edu/), converted into Sanger reads (groomer tool) and mapped to the Drosophila genome assembly (dm3) using, Bowtie. Mapped reads were subsequently filtered for Drosophila tRNAs sequences using LASTZ pairwise sequence alignment.
Genome Build:
mut_male_soma_2R_counts.txt: Drosophila melanogaster (Dm3)
|
| |
|
| Submission date |
Feb 21, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Schaefer Matthias |
| E-mail(s) |
matthias.schaefer@meduniwien.ac.at
|
| Organization name |
Medical University Vienna, Center for Anatomy & Cell Biology
|
| Department |
Cell and Developmental Biology
|
| Lab |
Schaefer Lab
|
| Street address |
Schwarzspanierstrasse 17-I
|
| City |
Vienna |
| State/province |
AT |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE35981 |
High-throughput sequencing of small RNAs (25-70 nt) from Drosophila wild-type and Dnmt2 mutants |
|
| Relations |
| Reanalyzed by |
GSM3276641 |
| SRA |
SRX121234 |
| BioSample |
SAMN00791497 |
