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| Status |
Public on Nov 05, 2012 |
| Title |
YW_SAMPLE1 |
| Sample type |
SRA |
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| Source name |
whole larvae, y w
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| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: y w
developmental stage: 3rd instar larvae
gender: male
tissue: whole body
sample type: control
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| Growth protocol |
Drosophila melanogaster was cultured at 25°C on a diet consisting of 0.8% (w/v) agar, 8% cornmeal, 1% soymeal, 1.8% dry yeast, 8% malt extract and 2.2% sugar-beet syrup, and was supplemented with 0.625% propionic acid and 0.15% Nipagin.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Sequencing libraries were generated according to the Illumina protocol for total RNA library preparation and loaded to Illumina flow cells (Illumina, San Diego, USA).
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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 |
Using the Illumina HiSeq 2000 instrument, 76 bp of sequence were read from one DNA end. Image analysis and base calling were done with the Illumina RTA software at runtime. The amount of data from raw FastQ files ranged between 25.87 and 39.33 million reads per sample. The sequences were mapped to the Drosophila genome assembly (version BDGP R5/dm3, April 2006) using Tophat, v.1.3.2 (Trapnell, 2009). The alignment output was processed using Cufflinks, v.1.1.0 (Trapnell, 2010), and the current UCSC annotation of the Drosophila genome (dm3). A single per-gene FPKM value provided by Cufflinks was used for the analysis rather than taking into account expression values for all isoforms of a particular gene. We included all genes for which FPKM of two replicates differed in the same direction from both control replicates at least 5% but did not exceed 6-fold between the two duplicates. To look for genes that were differentially expressed under the respective conditions, the average of the two duplicates was calculated.
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| Submission date |
Mar 08, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Mirka Uhlirova |
| E-mail(s) |
mirka.uhlirova@uni-koeln.de
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| Organization name |
CECAD, University of Cologne
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| Department |
Institute For Genetics
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| Street address |
Zülpicher Str. 47a
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| City |
Cologne |
| ZIP/Postal code |
50674 |
| Country |
Germany |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE36377 |
Activating transcription factor 3 regulates immune and metabolic homeostasis |
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| Relations |
| Reanalyzed by |
GSM3276792 |
| SRA |
SRX128179 |
| BioSample |
SAMN00809655 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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