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| Status |
Public on Apr 10, 2020 |
| Title |
CI-AKI Rep1_mRNA |
| Sample type |
SRA |
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| Source name |
kidney
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
tissue: kidney
age: three-month-old
Sex: male
disease state: contrast-induced acute kidney injury (CI-AKI)
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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). Afterwards, the total RNA was purified with RNAClean XP Kit (Cat A63987, Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set (Cat #79254, QIAGEN, GmBH, Germany).
Library was constructed in steps: rRNA removal, fragmentation, synthesis of 1st and 2nd strand of cDNA, end repairment, poly-A appending at 3'-end, adapter ligation, and enrichment. These steps were completed with VAHTS Total RNA-Seq Library Prep Kit for Illumina (Vazyme), Agencourt AMPure XP Beads (Beckman), SuperScript II Reverse Transcriptase (Invitrogen), Qubit dsDNA HS Array Kit (Invitrogen), and Agilent High Sensitivity DNA Kit (Agilent).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
Case1
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| Data processing |
Raw reads were preprocessed with Seqtk to filter out adapter sequences in reads, bases near 3'-end with quality value lower than 20, and reads of length smaller than 25, and reads of ribosome RNA.
Clean reads were aligned to reference genome (rn6) by Hisat2 (Ver2.0.4) with default parameters.
Gene expression was quantified and then normalized as FPKM(Fragments Per Kilobase of exon model per Million mapped reads). In this step, fragments of each gene were counted with Stringtie(version 1.3.0) and normalized into trimmed mean of M values (TMM), after which FPKM values of every gene were calculated by Perl scripts.
Genome_build: rn6
Supplementary_files_format_and_content: text file with FPKM and read count
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| Submission date |
May 07, 2019 |
| Last update date |
Apr 10, 2020 |
| Contact name |
Zhiqing Wang |
| E-mail(s) |
[email protected]
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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 |
GPL24688 |
| Series (2) |
| GSE130795 |
Co-expression Analysis Reveals Dysregulated miRNAs and miRNA-mRNA Interactions in the Development of Contrast-induced Acute Kidney Injury [mRNA] |
| 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 |
SAMN11585655 |
| SRA |
SRX5800740 |
| 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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