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| Status |
Public on Apr 10, 2020 |
| Title |
Control Rep2_miRNA |
| Sample type |
SRA |
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| Source name |
kidney
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: SD
tissue: kidney
age: three-month-old
Sex: male
disease state: control
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| Treatment protocol |
Rats were pretreated with intravenous injection of indomethacin (10mg/kg) and N-ω nitro-L-arginine methyl ester (10mg/kg) before contrast medium administration.
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| Growth protocol |
Rats were pretreated with water dehydration for 48 hours before the experiment, and were allowed to recover with free access to tap water after surgical procedure. Standard chow was allowed throughout the study.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with mirVana miRNA Isolation Kit (Cat #. AM1561, Austin TX, US) and its Standard Operating Protocol(SOP), which then experienced quality control with 2100 Bioanalyzer (Agilent Technologies Santa Clara, US).
Library was constructed in steps: 3'-end adapter ligation, 5'-end adapter ligation, reverse transcription, PCR amplification, size selection of cDNA library, and purification. These steps were completed with TruSeq Small RNA Sample Prep Kit (Illumina), T4 RNA Ligase 2 Truncated (BioLabs), SuperScript II Reverse Transcriptase (Invitrogen), 6% TBE Gel (1.0mm x 10well)(Invitrogen), Novex TBE Running Buffer (5X)(Invitrogen), Pellet Paint NF Co-precipitant (Novagen), Qubit dsDNA HS Assay Kit(Invitrogen), and Agilent High Sensitivity DNA Kit(Agilent).
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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 |
Raw reads were preprocessed with Fastx (Ver 0.0.13) to filter out adapter sequences in reads, bases near 3'-end with quality value lower than 10, and reads of length smaller than 10.
Clean reads were aligned to reference genome (rn6) by Bowtie (Ver0.12.7) with one mismatch allowed. After that, miRNA and other small RNAs were identified considering miRNA location from miRBase.
For expression quantification of miRNA, reads number of each miRNA was normalized into TMM (trimmed mean of M values), and then transformed into TPM (Transcripts per Million).
Genome_build: rn6
Supplementary_files_format_and_content: text file with abundance measurements
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| Submission date |
May 07, 2019 |
| Last update date |
Apr 10, 2020 |
| Contact name |
Zhiqing Wang |
| E-mail(s) |
wzq137747@163.com
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| Phone |
+8618905911812
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| Organization name |
900 Hospital of the Joint Logistics Team
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| Department |
Department of Cardiology
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| Street address |
NO. 156, North Xierhuan Road
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| City |
Fuzhou |
| State/province |
Fujian |
| ZIP/Postal code |
350025 |
| Country |
China |
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| Platform ID |
GPL18694 |
| Series (2) |
| GSE130796 |
Co-expression Analysis Reveals Dysregulated miRNAs and miRNA-mRNA Interactions in the Development of Contrast-induced Acute Kidney Injury [miRNA] |
| GSE130797 |
Co-expression Analysis Reveals Dysregulated miRNAs and miRNA-mRNA Interactions in the Development of Contrast-induced Acute Kidney Injury |
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| Relations |
| BioSample |
SAMN11585649 |
| SRA |
SRX5800732 |
| 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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