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| Status |
Public on May 30, 2018 |
| Title |
Dm310s KO replicate 2 |
| Sample type |
SRA |
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| Source name |
Dm310s KO
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain background: EP(2)2587 [P(3)l(2)05510EP2587; Szeged Stock Center)]
genotype/variation: Dm310s mutant
age: 3-5d adult
tissue: testes
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| Growth protocol |
Fruit flies were cultured under 25℃
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were dissected on dry ice, and RNA was harvested using Trizol reagent.
Libraries were prepared according to Illumina's instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
Gene expression in testes
2b_2
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| Data processing |
For RNA seq, raw data from RNA-seq were mapped to the D. melanogaster genome (r6.04), and normalized using Tophat (Trapnell, et al. 2009) and SeqMonk version 1.36.0 (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). The expression level of each gene was calculated in Reads Per Kilobase per Million (RPKM) and log2 transformed.
For small RNA seq, sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, and collapsed to the fasta format. The expression of mature miRNA was then measured using the Mapper and Quantifier modules of miRDeep2 version 2.0.0.7 (Friedlander, et al. 2012) with default parameters, normalized by the total reads matching all the miRNA precursors per library, and scaled as Reads Per Million (RPM).
Genome_build: FlyBase Drosophila melanogaster r6.04
Supplementary_files_format_and_content: gene expression, miRNA expression and fasta files include clean reads and raw read count;
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| Submission date |
Apr 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yixin Zhao |
| E-mail(s) |
[email protected]
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| Organization name |
Cold Spring Harbor Laboratory
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| Street address |
1 Bungtown Road
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| City |
Cold Spring Harbor |
| State/province |
NEW YORK |
| ZIP/Postal code |
11724 |
| Country |
USA |
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| Platform ID |
GPL9061 |
| Series (1) |
| GSE97364 |
Twin-miRs and their many weak targets |
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| Relations |
| BioSample |
SAMN06678418 |
| SRA |
SRX2702492 |
| 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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