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| Status |
Public on May 02, 2020 |
| Title |
RNA_Dpse_brain |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Drosophila pseudoobscura |
| Characteristics |
developmental time point: third instar wandering larvae
tissue: brain
genotype: Dpse\wild-type
stock: UCSD: 14011-0121.94
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| Treatment protocol |
Wandering 3rd instar larvae were dissected in PBS to extract the tissues of interest
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| Growth protocol |
All flies were raised at 25 degrees Celsius on standard fly food
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the RNAqueous micro kit (Ambion)
RNA libraries were generated for sequencing using standard Illumina TruSeq protocols
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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 |
Reads with residual adapter sequences were discarded (FastX cliper version 0.012 option -M15)
Reads were mapped against their own-species genome by TOPHAT v2.0 (default parameters)
Gene expression counts were computed by HTSeq (str=no) with the following genome annotations (D.melanogaster 5.46, D.simulans 1.4, D.yakuba 1.3, D.ananassae 1.3, D.pseudoobscura 2.30, D.willistoni 1.3, D.mojavensis 1.3 and D.virilis 1.2)
Genome_build: Drosophila melanogaster FB5, D.pseudoobscura FB2 and the rest of species, D.simulans, D.yakuba, D.ananassae, D.willistoni, D.mojavensis and D.virilis FB1
Supplementary_files_format_and_content: RNAseq samples:Gene counts in original species annotation and normalized data across species and tissues in D.melanogaster gene annotation.
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| Submission date |
Jul 23, 2014 |
| Last update date |
May 02, 2020 |
| Contact name |
Stein Aerts |
| Organization name |
KULeuven
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| Department |
Center for Human Genetics
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| Lab |
Laboratory of Computational Biology
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| Street address |
Herestraat 49
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| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
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| Platform ID |
GPL13310 |
| Series (1) |
| GSE59707 |
Evolutionary changes in cis regulation are associated with altered chromatin activity and gene expression levels in the Drosophila eye development (RNA-Seq) |
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| Relations |
| BioSample |
SAMN02934583 |
| SRA |
SRX660299 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1444032_RNA_Dpse_brain.counts.txt.gz |
66.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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