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| Status |
Public on Dec 05, 2017 |
| Title |
swine milk_2 |
| Sample type |
SRA |
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| Source name |
swine
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| Organism |
Sus scrofa |
| Characteristics |
breed: rongchang pig
tissue: milk
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer.s procedure. Thetotal RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA,USA) with RIN number >7.0. Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA). And then we performed the single-endsequencing (36 bp) on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China) following the vendor.s recommended protocol.
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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 |
Samples were placed in a refrigerator at -80C
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| Data processing |
the raw reads were subjected to the Illumina pipeline lter (Solexa 0.3), and thenthe dataset was further processed with an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) toremove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
unique sequences with length in 18~26 nucleotide were mapped to speci c species precursors in miRBase20.0 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 mappingto speci c species mature miRNAs in hairpin arms were identi ed as known miRNAs.
The unique sequences mappingto the other arm of known speci c species precursor hairpin opposite to the annotated mature miRNA-containing armwere considered to be novel 5p- or 3pderived miRNA candidates.
The remaining sequences were mapped to otherselected species precursors (with the exclusion of speci c species) in miRBase 20.0 by BLAST search, and the mappedpre-miRNAs were further BLASTed against the speci c species genomes to determine their genomic locations.
Theabove two we de ned as known miRNAs. The unmapped sequences were BLASTed against the speci c genomes,and the hairpin RNA structures containing sequences were predicated from the ank 80 nt sequences using RNAfoldsoftware (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi)
Genome_build: 84
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Dec 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhihong Liu |
| E-mail(s) |
liuzh7799@163.com
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| Organization name |
inner Mongolia agricultural university
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| Street address |
306 Zhao Wu Da
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| City |
Hohhot |
| ZIP/Postal code |
010018 |
| Country |
China |
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| Platform ID |
GPL10945 |
| Series (1) |
| GSE107652 |
Analyzing the Function of Exosome’s microRNA in Milk by Comparing the Expression of microRNA in Milk and Exosome |
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| Relations |
| BioSample |
SAMN08128402 |
| SRA |
SRX3441711 |
| 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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