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| Status |
Public on May 07, 2019 |
| Title |
uuo-day7-4 (miRNA-Seq) |
| Sample type |
SRA |
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| Source name |
uuo-day7, kidney
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| Organism |
Mus musculus |
| Characteristics |
strain: BALC/c
Sex: male
treatment: unilateral ureter obstruction
time: 7 days
tissue: kidney
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| Treatment protocol |
Unilateral ureter obstruction (UUO) model: Before surgery, mice were anaesthetized with an intraperitoneal injection of sodium pentobarbital (50 mg/kg of body weight), the left kidney was exposed via a flank incision and 3.0 silk suture thread was used to tie off the ureter at the lower pole. Before the obstruction and 3, 7, and 14 days later, mice were sacrificed, kidneys were removed and immediately snap frozen in liquid nitrogen.
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| Growth protocol |
Male BALC/c mice were obtained from Charles River Laboratories (USA). All experimental protocols concerning the use of laboratory animals were performed according to the NIH guidelines for the care and use of laboratory animals, and approved by the Institutional Animal Care and Use Committees (IACUC) of Harvard Medical School. Mice were housed in groups of three on a 12-h light/dark cycle with access to food and water ad libitum. At the age of 8-10 weeks they entered the experiment.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Qiagen’s miRNeasy Mini Kit. Quality and quantity of the RNA was assessed photometrically and with the Bioanalyzer (Agilent).
1 µg total RNA were transcribed utilizing Illumina‘s TruSeq Small RNA Library Prep Kit. Libraries were pooled and sequenced on Illumina’s NextSeq500 as single end, 75 bp reads.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
for small RNA seq
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| Data processing |
All samples were processed using a small RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/).
Quality control of the raw reads was performed as above for the RNA-seq data using FastQC and atropos.
Trimmed reads were aligned to miRBase v2124 to the specific species with seqbuster 25. In addition, the trimmed reads were aligned to the Mus musculus genome (version mm10) using STAR16,25.
The aligned reads were analyzed with seqcluster26 to characterize the whole small RNA transcriptome and classify reads into rRNA, miRNA, repeats, genes, tRNAs and others from the UCSCannotation 27.
Data were loaded into R using the bcbioSmallRna R package (https://github.com/lpantano/bcbioSmallRna) and isomiRs Bioconductor package 29,30 to get normalized expression values
Genome_build: mm10
Supplementary_files_format_and_content: normalized expression values
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| Submission date |
Aug 09, 2018 |
| Last update date |
May 08, 2019 |
| Contact name |
Lorena Pantano |
| E-mail(s) |
lpantano@iscb.org
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| Organization name |
Harvard Chan School of Public Health
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| Department |
Biostatistics
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| Lab |
Bioinformatic Core
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| Street address |
655 Huntington Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE118340 |
Multi Omics analysis of fibrotic kidneys in two mouse models [miRNA-Seq] |
| GSE118341 |
Multi Omics analysis of fibrotic kidneys in two mouse models |
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| Relations |
| BioSample |
SAMN09787159 |
| SRA |
SRX4524272 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3325599_day7_4-mirbase-ready.gtf.gz |
509.0 Kb |
(ftp)(http) |
GTF |
| GSM3325599_day7_4.mirna.txt.gz |
13.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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