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| Status |
Public on Jun 07, 2013 |
| Title |
wildtype rep1 |
| Sample type |
SRA |
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| Source name |
cn bw ovary
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| Organism |
Drosophila melanogaster |
| Characteristics |
genotype/variation: wildtype
tissue: ovary
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| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNA libraries from the cn bw control line, and from cuffwm25 homozygous ovaries were produced with the Small RNA Library Prep Kit (Illumina). Briefly, 20 μg total RNA extracted from the different genotypes was separated on a 15% denaturing polyacrylamide/urea gel electrophoresis (Invitrogen) for 1 h at 200 V. A gel slice corresponding to 18–30-nt-long RNAs was isolated and small RNAs were eluted and processed with the Small RNA Library Prep Kit as per the manufacturer's instructions. Small RNA libraries were subsequently sequenced on the Solexa Genome Analyzer II platform.
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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 |
smallRNA profiling
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| Data processing |
The Drosophila melanogaster genome assembly dm3 from UCSC genome browser, excluding ChrYhet and ChrUExtra,was used as the reference genome. Sequence reads were trimmed of their adaptor sequences with FASTX toolkit 0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/) with parameters -l 18 -Q33 -c -M 6 -a TCGTATGCCGTCTTCTGCTTGT. Bowtie 0.12.7 (http://bowtie-bio.sourceforge.net/index.shtml) was used to find exact matches in the genome for RNA reads with parameters -a -n 0 -e 1.
For the final processed WIG file, only uniquely mapped reads on genome were considered. For each biological replicate, the sequence read counts between wildtype and cuff mutant libraries were normalized by assuming the overall gene expression profiles were not affected between two conditions.
The WIG format files represented the sequence read counts in 100nts windows across each chromosome. Within each 100nts window, the first 50nts part represents the reads mapped on the plus strand and the last 50nts part represents the reads mapped on the minus strand. So, finally in the WIG file, window steps were set as 50nts with alternating counts on plus and minus strands.
Genome_build: dm3
Supplementary_files_format_and_content: UCSC WIG format
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| Submission date |
Jun 07, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Trudi Schupbach |
| E-mail(s) |
[email protected]
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| Organization name |
HHMI/Princeton University
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| Department |
Molecular Biology
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| Street address |
Washington Rd
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| City |
Princeton |
| State/province |
NJ |
| ZIP/Postal code |
08544 |
| Country |
USA |
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| Platform ID |
GPL9061 |
| Series (1) |
| GSE47738 |
The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline |
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| Relations |
| BioSample |
SAMN02192697 |
| SRA |
SRX297983 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1155652_Cn1.unique.wig.gz |
239.4 Kb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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