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Status |
Public on Nov 04, 2013 |
Title |
Dana_ovary_rep2 |
Sample type |
SRA |
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Source name |
ovary
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Organism |
Drosophila ananassae |
Characteristics |
strain: Drosophila Species Stock Center 14024-0371.13 genotype: wild type developmental stage: 6-10 day old adult tissue: ovary
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Growth protocol |
All flies were grown on cornmeal-molasses agar at 25C on 12 hour light/dark cycle at ~50% humidity.
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Extracted molecule |
polyA RNA |
Extraction protocol |
Virgin adult males and females were collected and aged 6-10 days before dissecting out testes or ovaries. All attached ducts were removed from the gonad tissue. Tissues were stored in RNAlater (Ambion) at -20C until RNA extraction. Immediately before RNA extraction RNAlater was removed by adding 1 mL RNase-free phosphate-buffered saline (PBS), centrifuging the sample 5,000 x g at 4 degrees C for 5 minutes, replacing the supernatant with 1 mL fresh PBS, centrifuging again, and replacing the supernatant with extraction buffer (XB) from the Arturus(R) PicoPure (R) kit according to the manufacturer's instructions. We included an on-column DNase digestion in the RNA extraction protocol. Libraries were constructed following the Illumina TruSeq RNA Library Construction Kit. Poly-A+ RNA was selected, reverse-transcribed using random (hexamer) priming, and the resulting cDNA fragments sheared to ~120-200 bp fragments. These fragments were used for adapter ligation and sequencing.
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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 |
genome_build: Drosophila ananassae release 1.3 (http://flybase.org) Raw data processing: Illumina's Real Time Analysis v 1.13 software was used to process sequencer images, call bases, and provide base quality scores Mapping reads to reference genomes: Bowtie v2.1.0 using default parameters and the appropriate reference genome. Differential expression analysis: Cufflinks v 2.1.0 Cuffdiff module, default parameters. Differential expression analysis: edgeR. Count values for genes were generated using HTseq v0.5.4p3 with options "-s no -m intersection-nonempty -a 1". Count values were full-quantile normalized within samples by gene-level GC content calculated from reference genome/annotation files and full-quantile normalized between samples before DE analysis. Supplementary_files_format_and_content: Cuffdiff files are native Cuffdiff v2.1.0 gene_exp.diff output files. In each case, sample_1 is testis and sample_2 is ovary. Value_1 and value_2 are then the normalized expression values (FPKM) of the locus that were used in the DE analysis. Please see the software manual for additional information on the file format. Supplementary_files_format_and_content: edgeR files are native output from edgeR's "topTags" subroutine. Information for all genes that were tested is included in this file, which consists of columns for gene ID, log2(normalized ovary expression level / normalized testis expression level), logCPM, likelihood ratios, P-values, and q-values. See the software manual for further information.
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Submission date |
Nov 04, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Maria D Vibranovski |
E-mail(s) |
mdv@ib.usp.br
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Organization name |
Universidade de Sao Paolo
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Department |
Genetics and Evolutionary Biology
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Street address |
Rua do Matao, 277
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City |
Sao Paulo |
ZIP/Postal code |
05508-090 |
Country |
Brazil |
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Platform ID |
GPL13309 |
Series (1) |
GSE52058 |
Identification of sex-biased genes in Drosophila using gonad RNAseq data |
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Relations |
BioSample |
SAMN02391496 |
SRA |
SRX373095 |
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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