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| Status |
Public on Feb 14, 2024 |
| Title |
testicular tissue, HO-1-1-1 (miRNA) |
| Sample type |
SRA |
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| Source name |
testicle
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: testicle
genotype: HO-1 knockout
Sex: Male
strain: Sprague Dawley
cell type: testis cell
treatment: the testicle suffered from reperfusion 3 days after ischemia 2 hours
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by using Trizol (Invitrogen,USA). The quantity and integrity of RNA yield was as-sessed by using the Qubit®2.0 (Life Technologies, USA) and Agilent 2200 TapeStation (Agilent Technologies, USA) separately. 1μg total RNA of each samples were used to prepare small RNA libraries by NEBNext® Multi- plex Small RNA Library Prep Set for Illumina (NEB,USA) according to manufacturer’s instructions.
The libraries were sequenced by HiSeq 2500 (Illumina,USA) with single-end 50bp at Ribobio Co. Ltd (Ribobio,China).
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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 processed by filtering out containing adapter, poly ’N’, low quality, smaller than 17nt reads by FASTQC to get clean reads. Mapping reads were obtained by mapping clean reads to reference genome of by BWA.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA by BLAST. The miRNA expression were calculated by RPM (Reads Per Million) values (PRM=(number of reads mapping to miRNA/ number of reads in Clean data)×106 ).
The expression levels were normalized by RPM, RPM is equal to (number of reads mapping to miRNA/ number of reads in Clean data)×10^6. Differential expression between two sets of samples was calculated by edgeR algorithm according to the criteria of |log2(Fold Change)|≥1 and P-value < 0.05.
TargetScan, miRDB, miRTarBase and miRWalk were used to predict targets gene of selected miRNA. KOBAS was used to further Gene Ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis.
Assembly: rn6
Supplementary files format and content: all.miRNA_expression.txt (RPMs)
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| Submission date |
Jul 05, 2023 |
| Last update date |
Feb 14, 2024 |
| Contact name |
Ning He |
| E-mail(s) |
[email protected]
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| Organization name |
The First Affiliated Hospital, Zhejiang University School of Medicine
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| Department |
Department of Urology
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| Street address |
No. 79 Qingchun Road
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310003 |
| Country |
China |
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| Platform ID |
GPL18694 |
| Series (2) |
| GSE236536 |
HO-1 attenuates testicular ischemia/reperfusion injury through activating the phosphorylated c-Jun-miR-221/222-TOX pathway [miRNA] |
| GSE237565 |
HO-1 attenuates testicular ischemia/reperfusion injury through activating the phosphorylated c-Jun-miR-221/222-TOX pathway |
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| Relations |
| BioSample |
SAMN36315345 |
| SRA |
SRX20904832 |
| 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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