|
| Status |
Public on Dec 10, 2020 |
| Title |
RAL-301_brain_T=0h9m_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
RAL-301_brain_T=0h9m
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: RAL-301
tissue: whole brain
time of harvesting: T=0h9m
replicate: 1
library: BRB9_A
bloomington: 25175
time series type: Single observation
|
| Growth protocol |
Flies were raised on standard food at 25 °C and under 12 hours light: 12 hours dark (LD) cycles.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standart Trizol extraction was performed, followed by Direct-zol™-96 RNA Purification (Zymo Resaearch) RNA purification
BRB-seq libraries were prepared according to Alpern et al 2019
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file:
raw_counts_all_samples.csv.gz
w1118_time_series_all_DGRPs_brain_norm.csv.gz
BRB9_Brain_n_25175
|
| Data processing |
Multiple fastq files for each library were merged by samtools v1.3,
after which they were subjected to demultiplexing using BRB-seq tools v1.1.
Then samples were mapped to the reference genome using STAR v.2.5.0b in the alignReads mode with the following parameters: --outFilterScoreMinOverLread 0.20, --outFilterMatchNminOverLread 0.20, --outFilterMultimapNmax 1.
RefSeq Genes annotation track (UCSC, annotation database for dm3) was used to index the reference genome.
Samtools was used to remove reads with an insert size > 1kb.
Number of reads falling into each of the 16,995 genes was counted using the Python package HTSeq v0.6.1
Samples with < 300,000 reads assigned to the genes (no feature, ambiguous, low quality, not aligned or mapped to the multiple locations reads were not considered) were excluded from the analysis
Genes, expressed in less than 80% of the samples were removed from the analysis.
The count table was quantile normalized with the voom function from the limma v3.32.5 package.
Batch effects from different libraries were removed with ComBat from SVA v3.24.4 package.
Genome_build: dm3, UCSC, BDGP Release 5, Apr 2006
Supplementary_files_format_and_content: *.csv.gz with raw (integer) count values for each sample as well as quantile-normalized and batch corrected counts:
raw_counts_all_samples: raw (integer) counts for all samples
w1118_time_series_brain_norm: normalized by voom and batch corrected by Combat counts for brain samples of the reference w1118 time series
w1118_time_series_fatbody_norm: normalized by voom and batch corrected by Combat counts for fat body samples of the reference w1118 time series
w1118_time_series_gut_norm: normalized by voom and batch corrected by Combat counts for gut samples of the reference w1118 time series
w1118_time_series_malpighiantubules_norm: normalized by voom and batch corrected by Combat counts for malpighiantubules samples of the reference w1118 time series
w1118_time_series_all_DGRPs_brain_norm: normalized by voom and batch corrected by Combat counts for brain samples of the reference w1118 time series and all DGRP samples
w1118_time_series_all_DGRPs_fatbody_norm: normalized by voom and batch corrected by Combat counts for fat body samples of the reference w1118 time series and all DGRP samples
w1118_time_series_all_DGRPs_gut_norm: normalized by voom and batch corrected by Combat counts for gut samples of the reference w1118 time series and all DGRP samples
DGRP-796_time_series_brain_norm: normalized by voom and batch corrected by Combat counts for brain samples of the DGRP-796 time series
DGRP-796_time_series_gut_norm: normalized by voom and batch corrected by Combat counts for fat body samples of theDGRP-796 time series
w1118_and_DGRP-796_time_series_brain_norm: normalized by voom and batch corrected by Combat counts for brain samples of the reference w1118 time series and DGRP-796 time series
w1118_and_DGRP-796_time_series_gut_norm: normalized by voom and batch corrected by Combat counts for gut samples of the reference w1118 time series and DGRP-796 time series
|
| |
|
| Submission date |
Feb 01, 2019 |
| Last update date |
Dec 10, 2020 |
| Contact name |
Bart Deplancke |
| E-mail(s) |
bart.deplancke@epfl.ch
|
| Organization name |
École polytechnique fédérale de Lausanne (EPFL)
|
| Department |
Biology
|
| Lab |
Laboratory of Systems Biology and Genetics
|
| Street address |
EPFL-SV-IBI-UPDEPLA, Station 19
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17275 |
| Series (1) |
| GSE126018 |
Extensive tissue-specific, circadian molecular variation in a Drosophila Genetic Reference Panel |
|
| Relations |
| BioSample |
SAMN10862401 |
| SRA |
SRX5324987 |
