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| Status |
Public on Aug 06, 2014 |
| Title |
SDY4_yak_MP2 |
| Sample type |
SRA |
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| Source name |
Whole body
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| Organism |
Drosophila yakuba |
| Characteristics |
strain: 14021-0261.00
developmental stage: white prepupae
Sex: male
tissue: Whole body
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| Growth protocol |
Flies were grown in standard corn meal medium, constant lighting conditions, and at 25⁰C. Larvae were raised under non-crowded conditions in medium with 0.05% bromophenol blue. Wandering larvae exhibiting dark blue gut, which corresponds to 18 hours before puparium formation, were collected, rinsed with water, and separated by sex. For the 0-1 hr white prepuparia, wandering larvae with light blue to white gut were separated by sex, placed in a Petri dish on damped light-wipe tissue until appropriate moment for collection. Samples were snap frozen in liquid nitrogen and stored at -80C until RNA isolation.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNAs were extracted and the enriched small RNAs were purified by miRVana miRNA isolation kit (Ambion Inc.)
The four nucleotide indexes: SDY_mel_ML1, ACTG; SDY1_mel_FL1, CTGA; SDY1_mel_MP1, TGAC; SDY1_mel_FP1, GACT; SDY3_mel_ML2, ACTG; SDY3_mel_MP2, TGAC; SDY3_sim_MP1, GACT; SDY3_yak_MP1, CGAT; SDY4_sim_MP2, ACTG; SDY4_yak_MP2, TGAC; SDY4_sim_ML1, GACT; SDY4_yak_ML1, CGAT. Adaptor-ligated cDNAs were prepared according to Illumina small RNA preparation protocol (Preparing Samples for Analysis of Small RNA Using the Oligo Only Kit, http://www.illumina.com). Briefly, 16-28nt small RNAs were size selected from a denaturing polyacrylamide gels, 5’ adaptors with four nucleotide indexes at the 3' end and 3’ adaptors were ligated using T4 RNA ligase (Ambion 2140) and the resulting molecules were purified by size selection from denaturing polyacrylamide gels after each ligation reaction. Four samples with different indexes were pooled for 3’ adaptor ligation and further preparation steps. The ligated small RNAs were reversed transcribed using Superscript II reverse transcriptase (Invitrogen 18064), subsequently PCR amplified with a Phusion high fidelity PCR DNA polymerase (Finnzymes F-506) through 10 cycles, and purified from denaturing polyacrylamide gels. The 5' adaptor sequence is 5'-GUUCAGAGUUCUACAGUCCGACGAUC-4nt RNA index-3'. The 3' adaptor sequence is 5'-P-UCGUAUGCCGUCUUCUGCUUGUidT-3'
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
SDY3_yak_MP1 and SDY4_yak_MP2 are from the same total RNA sample but different library preparations
processed data file: Reads_summary.xls, alignments_Dme_mirBase.txt, alignments_Dsi_mirBase.txt, alignments_Dya_mirBase.txt
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| Data processing |
Sequenced reads were sorted by index sequences, trimmed for adaptor and index sequences, masked for low-quality sequence, then mapped to known Dme, Dsi, and Dya miRNA hairpin sequences (miRBase release15) using bowtie-0.12.5 with parameters -faS -n 0 -l 99
Read number of 5' and 3' of miRNA hairpin sequene were counted separately
Genome_build: The known miRNA miRNA hairpin sequence of D. melanogaster, D. simulans, and D. yakuba in miRBase release15
Supplementary_files_format_and_content: The read number of 5' and 3' of miRNA for each sample is listed in Reads_summary.xls (i.e. read counts of different miRNAs in small RNA libraries from larva and pupa specimens). The alignments of reads from all libraries to the known miRNA hairpin sequences from miRBase release15 are provided in alignments_Dme_mirBase.txt (aligned to D. melanogaster known miRNAs), alignments_Dsi_mirBase.txt (aligned to D. simulans known miRNAs), and alignments_Dya_mirBase.txt (aligned to D. yakuba known miRNAs).
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| Submission date |
May 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Shu-Dan Yeh |
| E-mail(s) |
shudan.yeh@uci.edu
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| Organization name |
University of California, Irvine
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| Department |
Ecology and Evolutionary Biology
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| Lab |
Jose Ranz
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| Street address |
321 Steinhaus Hall
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| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697-2525 |
| Country |
USA |
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| Platform ID |
GPL11000 |
| Series (1) |
| GSE57438 |
Evolution of microRNA transcriptome at the onset of Drosophila metamorphosis |
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| Relations |
| BioSample |
SAMN02767771 |
| SRA |
SRX535442 |
| 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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