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| Status |
Public on Mar 20, 2015 |
| Title |
female_head_rep1 |
| Sample type |
SRA |
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| Source name |
head
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| Organism |
Musca domestica |
| Characteristics |
strain: CS (III^M)
Sex: female
tissue: head
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| Treatment protocol |
Dissections were performed on living, non-anesthetized 4-6 day old unmated adult flies. Gonad dissections were performed in Ringer's solution (182 mM KCl, 46 mM NaCl, 3 mM CaCl2, 10 mM Tris-Cl in ddH2O).
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| Growth protocol |
Flies were kept at 25C with a 12:12 hour light:dark cycle. Larvae were reared in media made with 1.8 L water, 500 g calf manna (Manna Pro, St. Louis, MO), 120 g bird and reptile litter wood chips (Northeastern Products, Warrensburg, NY), 60 g dry active baker's yeast (MP Biomedical Solon, OH), and 1.21 kg wheat bran (Cargill Animal Nutrition, Minneapolis, MN).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Samples were homogonized in TRIzol and RNA was extracted on QIAGEN RNeasy columns with gDNA elimination.
Barcoded mRNA-seq libraries were prepared using the Illumina TruSeq kit following the manufacturer's instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalls were performed using Casava 1.8.2
Reads were aligned to house fly genome assembly v2.0.2 and annotation release 100 using TopHat2 v2.0.8b and Bowtie v2.1.0.0 with the default parameters.
We tested for differential expression using the Cuffdiff2 program in the Cufflinks v2.2.1 package with the default parameters and a false discovery rate of 0.05.
Genome_build: Musca_domestica-2.0.2 (GCA_000371365.1)
Supplementary_files_format_and_content: alignments of reads to reference genome and annotation; expression level measurements (FPKM) and tests for differential expression
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| Submission date |
Mar 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard Meisel |
| Organization name |
University of Houston
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| Department |
Biology and Biochemistry
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| Street address |
3455 Cullen Blvd
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77204-5001 |
| Country |
USA |
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| Platform ID |
GPL19912 |
| Series (1) |
| GSE67065 |
Transcriptome Differences between Alternative Sex Determining Genotypes in the House Fly, Musca domestica |
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| Relations |
| BioSample |
SAMN03433664 |
| SRA |
SRX959571 |
| 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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