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| Status |
Public on Dec 17, 2021 |
| Title |
5d_10min_A |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain: OreR
genotype: wild type
age: 4-5 days
Sex: male
treatment: 10 min : Odor and light stimulated
tissue: brain
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit v2 was used with total RNA for the construction of sequencing libraries.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
For HiSeq2000: RTA v1.7, CASAVA v1.7 used for basecalling. For NextSeq500: RTA 2.0 used for basecalling.
Reads aligned to the latest release of each of the genomes used (dm6 for the Drosophila genome, GRCm38 for the Mus Musculus genome, and Araport11 for the Arabidopsis genome) and quantified with kallisto (Version: kallisto 0.43.1, Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, 525-527(2016), doi:10.1038/nbt.3519) . Only libraries for which we obtained >75 % alignment were used for downstream analysis.
Transcript counts were summarized to gene-level using tximport package (version 1.4.0).
For any instances of detected batch effects, we removed unwanted variation using RuvR in the RuvSeq package (version_1.10.0).
Differentially expressed gene (DEG) analysis was performed with the edgeR package (version 3.18.1), using low count filtering (cpm >0.5) and TMM normalization.
Genome_build: dm6 for the Drosophila genome, GRCm38 for the Mus Musculus genome, and Araport11 for the Arabidopsis genome
Supplementary_files_format_and_content: tab-delimited .tsv files including counts TPM normalized read counts for each sample
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| Submission date |
Dec 24, 2018 |
| Last update date |
Dec 17, 2021 |
| Contact name |
Christi Ann Scott |
| E-mail(s) |
[email protected]
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| Organization name |
University of California, Riverside
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| Department |
Molecular, Cell, and Systems Biology
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| Lab |
Anandasankar Ray
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| Street address |
3401 Watkins Drive
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| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92521 |
| Country |
USA |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE124343 |
Differential regulation of gene expression in neurons by spontaneous or sensory-driven activity and its dysregulation with aging |
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| Relations |
| BioSample |
SAMN10642573 |
| SRA |
SRX5179221 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3530176_5d_10min_A_abundance.tsv.gz |
406.2 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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