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Sample GSM5251262 Query DataSets for GSM5251262
Status Public on Nov 01, 2021
Title kidney_Female_006_rep3
Sample type SRA
 
Source name Kidney
Organism Rattus norvegicus
Characteristics strain: Fisher 344
tissue: Kidney
age (weeks): 6
Sex: Female
replicate: 3
Treatment protocol Each whole organ was individually ground into a fine powder
Growth protocol pair-housed under standard conditions
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from ~30 mg of ground tissue by using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol, including treatment with DNase.
Small RNA libraries were constructed using Illumina TruSeq Small RNA Library Prep kit.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
 
Data processing The adapter sequences were removed with fastp 0.23.2 software (http://opengene.org/fastp/fastp.0.23.2), followed by a quality filter and a length filter. Reads with more than 2 “N” bases were discarded. The clipped reads with length between 16 and 35 nt were retained for alignment to various transcript types, including miRNA (miRbase v22.1, http://www.mirbase.org/), piRNA (piRBase, http://www.regulatoryrna.org/database/piRNA/download.html), tRNA (GtRNAdb, http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/eukaryota/Rnorv7/Rnorv7-seq.html), other RNA (NCBI transcriptome, https://www.ncbi.nlm.nih.gov/genome/73), and the rat genome (Rn7, https://hgdownload.soe.ucsc.edu/downloads.html#mammals). The alignment was performed with Bowtie 1.3.1 (http://bowtie-bio.sourceforge.net/manual.shtml) with less than 2 mismatched bases allowed.
miRDeep2.0.1.3 was used for novel miRNA predicting and mapping.
Genome_build: rat genome rn7 download from UCSC and miRBase v22.1.
Sequence of novel miRNAs are available in file on series record.
Supplementary_files_format_and_content: read count
 
Submission date Apr 17, 2021
Last update date Feb 11, 2022
Contact name Leming Shi
E-mail(s) lemingshi@fudan.edu.cn
Phone +86-18616827008
Organization name Fudan University
Department School of Life Sciences
Lab Center for Pharmacogenomics
Street address 2005 Songhu Road
City Shanghai
ZIP/Postal code 200438
Country China
 
Platform ID GPL18694
Series (1)
GSE172269 Landscape of rat microRNA BodyMap across 11 organs, four ages, and two sexes
Relations
BioSample SAMN18789402
SRA SRX10627346

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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