|
| Status |
Public on Feb 01, 2019 |
| Title |
wt control 0 hours OS 1 |
| Sample type |
SRA |
| |
|
| Source name |
male fly head
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: wildtype control
treatment: no treatment
duration: 0 hours post treament
age: 5-9 days
tissue: head
|
| Treatment protocol |
Flies (5-9 days) were transferred to paraquat containing food (50 mM) and incubated at 25 °C and 70 % humidity. At each time point, samples for RNA-seq were collected by flash freezing flies in liquid nitrogen followed by vortexing and filtering through a series of sieves to isolate heads from other body parts.
|
| Growth protocol |
Flies were reared on standard medium (cornmeal/sugar/yeast) at 25 °C and 70 % humidity with a 12-h light/dark cycle. Flies were collected after eclosion and allowed to recover from CO2 exposure for 5 days prior to paraquat exposure.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
200 fly heads per sample were used for total RNA extraction using QIAGEN lipid mini tissue kit.
mRNA libraries where prepared from 100 ng total RNA using Truseq RNA library prep v2 (Illumina). Samples where indexed and 4 samples where multiplexed on one sequencing lane. Samples 1, 2, 4 and 5 contain True-seq barcode 4, samples 19, 20, 22, 23 contain True-seq barcode 5 and samples 25, 26, 28, 29 contain True-seq barcode 6.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
G9a wild type heads after 0 hours oxidative stress exposure (paraquat)
|
| Data processing |
Sequenced reads were aligned with Burrows-Wheeler algorithm (BWA) (Li & Durbin, 2010) to the Drosophila reference genome (BDGP.5, http://www.fruitfly.org/).
Per gene read counts were generated with HTSeq count (Anders et al, 2015) with following paramenters: intersection non-empty, non-stranded, quality filter = 15.
DESeq (Anders & Huber, 2010) was used to obtain library size-normalized read counts and to calculate differential expression of genes in 4 pairwise comparisons: 0 h versus 6 h and 0 h versus 12 h after OS in both G9a mutants and controls (fold change ≥1.5, adjusted p-value≤ 0.05, Benjamini-Hochberg).
Genome_build: Drosophila_melanogaster.BDGP5.70.gtf
Supplementary_files_format_and_content: Tab delimited file table of normalized count data. Tab delimited DESeq output files of 4 pairwise comparisons: wildtype 0 hours versus wildtype 6 hours (wt0VSwt6) and 12 hours (wt0VSwt12) after paraquat exposure. G9aDD1 mutant 0 hours versus G9aDD1 mutant 6 hours (mt0VSmt6) and 12 hours (mt0VSmt12) after paraquat exposure.
|
| |
|
| Submission date |
Feb 06, 2018 |
| Last update date |
Feb 01, 2019 |
| Contact name |
Human Riahi Asl |
| E-mail(s) |
[email protected]
|
| Phone |
0031619898485
|
| Organization name |
Radboud UMC
|
| Department |
Human Genetics
|
| Lab |
Drosophila model of brain disorders
|
| Street address |
Geert Grooteplein Zuid 10
|
| City |
Nijmegen |
| State/province |
Gelderland |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE110240 |
Title: Transcriptional profiles (mRNA-seq) of Drosophila G9aDD1 mutants and control during 0, 6 and 12 hours of paraquat oxidative stress exposure. |
|
| Relations |
| BioSample |
SAMN08472947 |
| SRA |
SRX3654323 |
