|
| Status |
Public on Oct 19, 2016 |
| Title |
w1118-hs6-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: w1118
replic: Replic 1
time point after hs: 6h
|
| Treatment protocol |
Heat shock 38.5C, 30 min.
|
| Growth protocol |
Standard yeast medium, 25C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 3-5 day old females after 1h, 6h and 24h of recovery at 25C after heat shock treatment
Total RNA was isolated using Tri-reagent (Sigma-Aldrich, USA). A total of 25µg of total RNA were separated using 15% polyacrylamide gel electrophoresis containing 8 M of urea. After incubation in ethidium bromide solution (0.5 mkg/ml), gel fragments corresponding to small RNAs fraction were excised. We used chemically synthesized RNAs (Syntol, Russia) corresponding to 21 and 27 nucleotides as size markers. Cloning of small RNA libraries were conducted using the Illumina TruSeq Small RNA Prep Kit (Illumina, USA) according to the manufacturer’s protocol. Each sample was made in two biological replicates. Sequencing of small RNAs was performed on an Illumina HiSeq 2000 (Illumina, USA).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
After adapter (5'-TGGAATTCTCGGGTGCCAAGG) trimming and quality filtering, small RNA-seq reads were mapped to dm3 genome assembly with Bowtie 1.0.0 as bowtie -v 0 --all —al.
After mapping reads were annoted with BedTools (2.22.0) and using miRBase (v.19) annotaion.
Genome_build: dm3
|
| |
|
| Submission date |
Jan 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sergei Ryazansky |
| E-mail(s) |
[email protected]
|
| Phone |
+7-499-196-81-73
|
| Organization name |
Institute of Molecular Genetics
|
| Department |
Department of Molecular Genetics of Cell
|
| Street address |
Kurchatov sq., 2
|
| City |
Moscow |
| ZIP/Postal code |
123182 |
| Country |
Russia |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE76844 |
Interplay between RNA interference and heat shock response systems in Drosophila melanogaster |
|
| Relations |
| BioSample |
SAMN04407954 |
| SRA |
SRX1530055 |
