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| Status |
Public on Jul 04, 2019 |
| Title |
5 hpo embryos |
| Sample type |
SRA |
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| Source name |
5 post-oviposition (hpo) embryos
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| Organism |
Bactrocera dorsalis |
| Characteristics |
tissue: embryos
age: 5 post-oviposition (hpo)
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| Extracted molecule |
total RNA |
| Extraction protocol |
5, 6 and 7 post-oviposition (hpo) embryos were collected and immediately stored in RNAlater® Solution (Ambion). Total RNAs were extracted using Trizol reagent (Invitrogen, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with total RNA for the construction of sequencing libraries.
Small RNA libraries were generated from the three samples using the Illumina Truseq Small RNA Preparation kit according to Illumina’s TruSeq Small RNA Sample Preparation Guide. The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument. Raw sequencing reads were obtained using Illumina’s Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70). A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis. Degradome library was constructed following with methods previously described by German et al.(2008).CleaveLand3.0 and LC Science’s ACGT301-DGEv1.0 program were used to detect potentially sliced targets of known and novel miRNA.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The raw reads were subjected to the Illumina pipeline filter (Solexa 0.3), and then the dataset was further processed with an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 20.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identied as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 20.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi).
The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (<=12) (2) number of base pairs in the stem region of the predicted hairpin (>=16) (3) cutoff of free energy (kCal/mol <=15) (4) length of hairpin (up and down stems + terminal loop >=50) (5) length of hairpin loop (<=200). (6) number of nucleotides in one bulge in mature region (<=4) (7) number of biased errors in one bulge in mature region(<=2) (8) number of biased bulges in mature region (<=2) (9) number of errors in mature region (<=4) (10) number of base pairs in the mature region of the predicted hairpin (>=12) (11) percent of mature in stem (>=80).
Genome_build: ASM78921v1
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| Submission date |
Jul 18, 2018 |
| Last update date |
Jul 04, 2019 |
| Contact name |
Wei Peng |
| E-mail(s) |
pengweijack@163.com
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| Organization name |
Huazhong Agricultural University
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| Street address |
Shizishan Street No. 1, Hongshan District, Wuhan,Hubei 430070, P.R. China
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| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platform ID |
GPL21756 |
| Series (1) |
| GSE117310 |
The widely conserved microRNA, miR-1-3p, is a male-determining factor in the oriental fruit fly, Bactrocera dorsalis |
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| Relations |
| BioSample |
SAMN09689453 |
| SRA |
SRX4404378 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3290897_5_hpo_embryos_known_miRNAs.xls.gz |
18.9 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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