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| Status |
Public on Nov 28, 2008 |
| Title |
Ovary_rep1_wK(fem)_x_w1118(male)_F1 |
| Sample type |
SRA |
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| Source name |
Ovary, female progeny of a cross between strain wK (female) and w1118 (male), 3-5 days old, 21 degrees C
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| Organism |
Drosophila melanogaster |
| Characteristics |
female progeny of a cross between strain wK (female) and w1118 (male), females, 3-5 days old
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| Treatment protocol |
Trizol/Phenol Cholorofom extractions
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| Growth protocol |
21 or 24 degrees C
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
none
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| Data processing |
The 36nt long Illumina reads were stripped of the 3’ linker and the resulting small RNA sequences were mapped to the Release 5 genome excluding the Uextra portion. Only reads matching the fly genome 100% were used for further analysis. For annotation, we used Flybase for protein coding genes, UCSC for non-coding RNAs and transposons/repeats (repeat masker tracks) and the most recent miRNA catalog. To control for sequencing depth, small RNA counts were normalized to the same total number after subtracting those matching abundant cellular RNAs such as rRNAs and tRNAs. For the piRNA analysis, we selected small RNAs, which exceeded 22 nt in length and were not annotated as miRNA, tRNA, rRNA, snoRNA, snRNA or smRNA.
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| Submission date |
Oct 07, 2008 |
| Last update date |
May 15, 2019 |
| Contact name |
Colin Dean Malone |
| E-mail(s) |
colin.malone@med.nyu.edu
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| Phone |
708-602-2170
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| Organization name |
NYU Medical Center
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| Department |
Skirball Institute - Developmental Genetics
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| Lab |
Lehmann Lab
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| Street address |
NYUMC, Skirball Institute, 540 1st Ave, 4-10
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platform ID |
GPL9061 |
| Series (1) |
| GSE13081 |
An epigenetic role for maternally inherited piRNAs in transposon silencing |
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| Relations |
| SRA |
SRX003133 |
| BioSample |
SAMN02195719 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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