GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM3262317

Query DataSets for GSM3262317

Status

Public on Jul 10, 2018

Title

ZDF + Vehicle - Sample 3

Sample type

SRA

Source name

ZDF + Vehicle, liver

Organism

Rattus norvegicus

Characteristics

strain: ZDF-Leprfa/Crl
tissue: Liver
age: 8-weeks
phenotype: Obese
agent: Vehicle

Extracted molecule

total RNA

Extraction protocol

livers were removed, flash frozen in liquid nitrogen, and RNA was harvested using Norgen Total RNA isolation kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

miRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina HiSeq 2500

Description

Veh_3259_1

Data processing

All reads ≥16nts in length were aligned to the rat genome (Rnor5.0) by Bowtie1(v1.1.2)[30] allowing one mismatch. DEseq2 (v1.18.1)[31] was used to identify significant (p<0.05) differentially (absolute fold change >1.5) expressed liver miRNAs.
miRNAs that were detected in the sequencing experiment are reported in the processed data file (401 miRNAs). miRNA were considered "detectable" and included in the analysis is 50% of sample had > 5 reads (median 5 reads).
Genome_build: Rnor5.0
Supplementary_files_format_and_content: .csv file includes RPKM values for each Sample

Submission date

Jul 09, 2018

Last update date

Jul 10, 2018

Contact name

Leslie Roteta Sedgeman

Organization name

Vanderbilt University

Street address

2220 Pierce Avenue

City

Nashville