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| Status |
Public on Sep 20, 2017 |
| Title |
S12_heads_RNAseq |
| Sample type |
SRA |
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| Source name |
Male heads
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: head
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| Growth protocol |
For each sample, 5 heads or whole bodies were collected from 3-5 day old male adult flies that were raised at 25˚C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNAdvance magnetic beads (Agencourt), treated using TURBO DNase (Thermo Fisher Scientific), and depleted of ribosomal RNA.
Libraries produced using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems) were sequenced on an Illumina NextSeq 500 Sequencer using paired-end 76-bp cycles.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
rRNA-depleted RNA
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| Data processing |
gene expression: fastx_trimmer was used to trim the 75th and 76th base from reads.
gene expression: Trimmed reads were mapped using TopHat and version 5.53 D. melanogaster Flybase gene annotations, using the parameters "-N 5 --segment-mismatches 3 --read-edit-dist 5".
gene expression: Read counts were obtained using featureCounts from the Subread package.
gene expression: DESeq2 was used to obtain gene expression levels.
Genome_build: dm3 (BDGP release 5)
Supplementary_files_format_and_content: gene expression: The processed data files contain gene expression counts for each sample that served as input for DESeq2. The tab-delimited columns are formatted as: gene name, gene expression count.
RNA editing levels: fastx_trimmer was used to trim the 75th and 76th base from reads.
RNA editing levels: Trimmed reads were mapped to the dm3 genome in addition to 70bp of exonic sequence surrounding known splice junctions using BWA, with the default settings.
RNA editing levels: Duplicate reads were marked using Picard, and duplicate and unmapped reads were removed using Samtools, as well as reads with a mapping quality less than 10
RNA editing levels: Fly RNA editing sites were downloaded from the RADAR database (www.rnaedit.com)
RNA editing levels: RNA editing levels were calculated as the number of 'G' reads divided by the number of 'A' and 'G' reads at each site, for bases that had a quality score of at least 20.
Supplementary_files_format_and_content: RNA editing levels: The processed data files contain editing levels for each Evolution Canyon fly line. The tab-delimited columns are formatted as: chromosome, position, number of A reads, number of G reads, 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) |
| GSE104073 |
Measuring gene expression and RNA editing in Drosophila adapting to divergent microclimates |
| GSE104085 |
Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates |
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| Relations |
| Reanalyzed by |
GSM3284089 |
| BioSample |
SAMN07679426 |
| SRA |
SRX3202314 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2788975_S12_heads_GeneExpression.txt.gz |
70.5 Kb |
(ftp)(http) |
TXT |
| GSM2788975_S12_heads_RNAseq_EditingLevels.txt.gz |
36.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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