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Sample GSM3964299 Query DataSets for GSM3964299
Status Public on Jan 21, 2020
Title Dox_3: miR-26a_Dox_3
Sample type SRA
 
Source name Cultured primary SVFs from WAT
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: stromal vascular fraction
genotype/variation: M2rtTA;eGFP.miR-26a +Doxycycline
age: 6 weeks
Treatment protocol miR-26a transgenic mice were cultured in vitro with or without doxycycline (1mg/ml) for 4 days in culture.
Growth protocol Primary wild-type and TKO SVFs were isolated and cultured to confluency prior to RNA isolation. miR-26a transgenic SVFs were grown to confluency in presence or absence of doxycycline (1mg/ml) for 4 days.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from i) wild-type and miR-26-TKO (mR-26a-1-/-; miR-26a-2-/-; miR-26b-/-) primary SVFs or ii) miR-26a transgenic primary SVFs with and without doxycycline treatment using the miRNeasy Mini Kit (Qiagen) including an on-column DNAse I digestion step.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and sequenced using the 75 bp single-read protocol on a NextSeq 500 platform (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Treated with 1mg/ml of doxycycline for 4 days in vitro
Data processing Quality assessment of the RNA-seq data was performed using NGS QC Toolkit (v2.3.3). Reads with more than 30% of nucleotides with a Phred quality score of less than 20 were removed from further analysis.
Quality-filtered reads were aligned to the mouse reference genome GRCm38 (mm10) using Tophat2 (v2.0.12) with default settings.
Aligned reads were counted per gene using featureCount (v1.4.6).
Differential gene expression analysis was carried out using EdgeR (v3.8.6).
Fragments per kilobase million (FPKM) were obtained using Stringtie (v1.2.2).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files including gene ID and FPKM
 
Submission date Jul 23, 2019
Last update date Jan 21, 2020
Contact name Joshua Mendell
E-mail(s) joshua.mendell@utsouthwestern.edu
Organization name UT Southwestern Medical Center
Department Molecular Biology
Street address 6000 Harry Hines Blvd., NA6.200A
City Dallas
State/province TX
ZIP/Postal code 75390-9148
Country USA
 
Platform ID GPL19057
Series (1)
GSE134736 miR-26 suppresses adipocyte progenitor differentiation and fat production by targeting Fbxl19
Relations
BioSample SAMN12344322
SRA SRX6492413

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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