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| Status |
Public on Sep 20, 2017 |
| Title |
S5-2_25C_mmPCR |
| Sample type |
SRA |
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| Source name |
Male whole body
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Whole body
replicate: 2
temperature: 25˚C
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| Growth protocol |
Whole bodies were collected from 3-5 day old male adult flies raised at 25˚C or 18˚C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Agencourt RNAdvance Tissue Kit, followed by DNAse I treatment (Thermo Fisher Scientific). cDNA synthesis was performed using the iScript Advanced cDNA synthesis kit (BioRad).
Libraries were prepared by pooling all of the PCR products for a particular sample and barcoding them uniquely using a 15 cycle PCR reaction.
microfluidic multiplex PCR (mmPCR-seq)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
RNA editing comparisons between populations: The first 19 bases of the read (representing the primer sequence) and the bases after the 143rd base were trimmed.
RNA editing comparisons between populations: Trimmed reads were mapped to the dm3 genome in addition to 120bp of exonic sequence surrounding known splice junctions using BWA, allowing 6 mismatches per read.
RNA editing comparisons between populations: Fly RNA editing sites were downloaded from the RADAR database (www.rnaedit.com)
RNA editing comparisons between populations: RNA editing levels were calculated as the percentage of G reads at each site.
Genome_build: dm3 (BDGP release 5)
Supplementary_files_format_and_content: RNA editing comparisons between populations: The processed data files contain editing levels for each Evolution Canyon fly line, including replicates. The tab-delimited columns are formatted as: chromosome, position, number of edited reads, sequencing coverage, editing level. Editing sites for which there was no coverage are not included.
RNA editing comparisons between those temperatures: The first 19 bases of the read (representing the primer sequence) and the bases after the 75th base were trimmed.
RNA editing comparisons between those temperatures: Trimmed reads were mapped as single-end reads to the dm3 genome in addition to 52bp of exonic sequence surrounding known splice junctions using BWA, allowing 6 mismatches per read.
RNA editing comparisons between those temperatures: Fly RNA editing sites were downloaded from the RADAR database (www.rnaedit.com)
RNA editing comparisons between those temperatures: RNA editing levels were calculated as the percentage of G reads at each site.
Supplementary_files_format_and_content: RNA editing comparisons between those temperatures: The processed data files contain editing levels for each Evolution Canyon fly line, including replicates. The tab-delimited columns are formatted as: chromosome, position, number of edited reads, sequencing coverage, editing level. Editing sites for which there was no coverage are not included.
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| Submission date |
Sep 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jin Billy Li |
| E-mail(s) |
[email protected]
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| Organization name |
Stanford University
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| Department |
Genetics
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| Street address |
300 Pasteur Drive, Alway M-341
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL19132 |
| Series (2) |
| GSE104084 |
Measuring RNA editing through mmPCR-seq in Drosophila adapting to divergent microclimates and raised at different temperatures |
| GSE104085 |
Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates |
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| Relations |
| BioSample |
SAMN07679812 |
| SRA |
SRX3202648 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2789342_S5-2_25C_TrimmedMore_mmPCR_EditingLevels.txt.gz |
8.1 Kb |
(ftp)(http) |
TXT |
| GSM2789342_S5-2_25C_mmPCR_EditingLevels.txt.gz |
8.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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