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| Status |
Public on Oct 13, 2016 |
| Title |
4.Ctrl |
| Sample type |
SRA |
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| Source name |
whole adult male flies
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| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: w[1118] / Y ; c564 / +
age: 5-10 days posteclosion
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
For each sample, 5 male flies were lysed in 200 ul TRIzol reagent and total RNA was extracted according to the manufacturer's instructions, followed by an extra round of ethanol precipitation.
Libraries were prepared using Illumina TruSeq Stranded mRNA v2, with the following changes from the manufacturer’s protocol: starting samples were 250ng total RNA; fragmentation was performed for 10 minutes at 94°; no spike-ins were used; and 14 cycles of PCR were used to enrich libraries. Libraries were sequenced on an Illumina NextSeq 500 using v1 chemistry.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
control replicate 4
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| Data processing |
Illumina RTA software was used for basecalling.
Sequenced reads were demultiplexed and adaper trimmed using Illumina bcl2fastq software, then mapped to Drosophila melanogaster genome version 6.26 using STAR 2.4.0j. Command line: STAR --outSJfilterCountUniqueMin 5 2 2 2 --outSJfilterCountTotalMin 5 2 2 2 --outFilterType BySJout
Mapped reads were associated with genes using the FeatureCounts command in Rsubread. Differentially-expressed genes were identified using Limma.
Genome_build: BDGP6.26
Supplementary_files_format_and_content: tab-delimited text spreadsheet of non-normalized counts mapping to genes
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| Submission date |
Apr 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Marc Dionne |
| E-mail(s) |
[email protected]
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| Organization name |
Imperial College London
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| Department |
Life Sciences
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| Street address |
Level 0, Flowers Building
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| City |
London |
| ZIP/Postal code |
SW7 2AZ |
| Country |
United Kingdom |
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| Platform ID |
GPL19132 |
| Series (1) |
| GSE80318 |
Effect of Mef2 knockdown in Drosophila fat body |
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| Relations |
| Reanalyzed by |
GSM3278885 |
| BioSample |
SAMN04858454 |
| SRA |
SRX1706922 |
| 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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