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| Status |
Public on Sep 27, 2018 |
| Title |
Ser_Ex_miRNA |
| Sample type |
SRA |
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| Source name |
Serum derived exsome
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| Organism |
Sus scrofa |
| Characteristics |
breed: Rongchang
age: postnatal day 180
tissue: Serum
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| Extracted molecule |
total RNA |
| Extraction protocol |
Exsome was collected unsing RiboTM Exosome Isolation Reagent, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.In general, approximately 15 ug of small RNA-enriched total RNA was prepared for High-throughput sequencing. In brief, High-throughput sequencing was performed as following successive step: For each library, the small RNA ranged from 14 to 40 nt were purified by polyacrylamide gel electrophoresis (PAGE) and ligated with proprietary adaptors (Illumina). Then the modified small RNA was reverse transcribed and amplified by RT-PCR. Finally, the enriched cDNA were sequenced on Genome Analyzer II (GAI, Illumina, San Diego, CA, USA) according to manufacturer instructions.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
microRNA
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| Data processing |
Illumina bcl2fastq 2.17 software used for basecalling.All reads were counted and the identical reads were combined into a single kind. The raw reads were subjected to a series of additional strict filters (such as the digital filters of base-call quality, reads length, and sequence comparison) with acceptance criteria derived from the statistics of mammalian miRNAs in miRBase 21.0. The reads originated from porcine known classes of RNAs (i.e., mRNA; rRNA, tRNA, snRNA, and snoRNA; and repetitive sequence elements) were also filtered.In addition, to ensure higher reliability of the reported results, only the reads that were observed more than 10 times for each library were used in subsequent analyses.
To conduct differential analysis, miRNA read in each library was normalized to obtain the expression of transcripts per million (RPM).
Genome_build: Genome database:Sus scrofa (Sscrofa10.2); miRbase version: V21.0
Supplementary_files_format_and_content: identified miRNAs in each library with reads and normalized data
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| Submission date |
Sep 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jie Zhang |
| E-mail(s) |
zhangjie813@163.com
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| Phone |
023-46751588
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| Organization name |
Southwest University
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| Department |
College of Animal Science
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| Lab |
Institute of Animal Genetics & Breeding
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| Street address |
Xueyuan road #160
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| City |
Rongchang |
| State/province |
Chongqing |
| ZIP/Postal code |
402460 |
| Country |
China |
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| Platform ID |
GPL10945 |
| Series (1) |
| GSE87381 |
MicroRNA spectrum of porcine serum, plasma, semen, urine and bile exsome |
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| Relations |
| BioSample |
SAMN05829252 |
| SRA |
SRX2193258 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2329996_Serum_miR_list.txt.gz |
2.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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