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Sample GSM3325589 Query DataSets for GSM3325589
Status Public on May 07, 2019
Title normal-1 (miRNA-Seq)
Sample type SRA
 
Source name normal, kidney
Organism Mus musculus
Characteristics strain: BALC/c
Sex: male
treatment: no treatment
time: control
tissue: kidney
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.
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.
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.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NextSeq 500
 
Description for small RNA seq
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
 
Submission date Aug 09, 2018
Last update date May 08, 2019
Contact name Lorena Pantano
E-mail(s) lpantano@iscb.org
Organization name Harvard Chan School of Public Health
Department Biostatistics
Lab Bioinformatic Core
Street address 655 Huntington Ave
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
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
Relations
BioSample SAMN09787169
SRA SRX4524262

Supplementary file Size Download File type/resource
GSM3325589_normal_1-mirbase-ready.gtf.gz 330.7 Kb (ftp)(http) GTF
GSM3325589_normal_1.mirna.txt.gz 13.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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