|
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).
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|
|
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
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|
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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 |