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| Status |
Public on Dec 31, 2018 |
| Title |
SI-10 (A_1) |
| Sample type |
SRA |
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| Source name |
spleen
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| Organism |
Sus scrofa |
| Characteristics |
group: infected
age: post inoculation day 10
tissue: spleen
strain: Landrace
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| Extracted molecule |
total RNA |
| Extraction protocol |
Spleens were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Three individuals’ RNA samples, of the same group at each time point were equally mixed to generate an RNA pool. A total amount of 3 μg total RNA per pool was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.).
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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 |
Illumina Casava1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for poly-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads sequence, and reads with lengths shorter than 18 nt or longer than 35 nt were filtered, then mapped to Sscrofa 10.2 whole genome using bowtie-v0.12.9 with parameters -v 0 -k 1 for alignment analysis of short sequences.
Tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA and snoRNA were removed by mapping to RepeatMasker open-4.0.3, Rfam database (http://rfam.xfam.org/) or those types of data from pig.
Known miRNA were identified from the mapped sRNA tags in miRBase 20.0 (http://www.mirbase.org/), and the available software miREvo_v1.1, mirdeep2_0_0_5 and ViennaRNA-2.1.1 were integrated to predict novel miRNA
MiRNA which might have base edit could be detected by aligning all the sRNA tags to mature miRNA, allowing one mismatch
Known miRNA used miFam.dat (http://www.mirbase.org/ftp.shtml) to look for families; novel miRNA precursor was submitted to Rfam (http://rfam.sanger.ac.uk/search/) to look for Rfam families.
MiRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010): Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Genome_build: Sscrofa 10.2
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.
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| Submission date |
Apr 13, 2018 |
| Last update date |
Dec 31, 2018 |
| Contact name |
Hou Zhaofeng |
| E-mail(s) |
hzf2006sj@163.com
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| Organization name |
Yangzhou University
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| Street address |
No. 12, Wenhui East Road
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| City |
Yangzhou |
| State/province |
Jiangsu |
| ZIP/Postal code |
225009 |
| Country |
China |
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| Platform ID |
GPL19176 |
| Series (1) |
| GSE113130 |
Comparison of microRNA expression profiling in pig spleens among three time points after infection by Chinese I genotype strain of Toxoplasma gondii |
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| Relations |
| BioSample |
SAMN08930036 |
| SRA |
SRX3933814 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3097743_A_1.txt.gz |
16.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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