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Sample GSM4314352 Query DataSets for GSM4314352
Status Public on Dec 15, 2022
Title T2D+AAV-dnMCUb2
Sample type SRA
 
Source name primary mouse heart tissue
Organism Mus musculus
Characteristics disease state: Type 2 diabetes (T2D)
transgene over expression: AAV dnMCUb
genotype/variation: T2D mice overexpressing dnMCUb
Treatment protocol MCUb was cloned from mouse heart and subsequently a dominant negative MCUb was generated by introducing two point mutations (CTG>CAG and TGT>AGT) resulting in W246R and V251E using the QuikChange Site-Directed Mutangenesis kit (Stratagene). In vivo AAV transgene delivery was performed by direct jugular vein injection as already described (Suarez J, JBC 2018). Empty AAV (AAV-Empty) or AAV encoding C-terminal FLAG-tagged murine MCUb W246R/V251E (AAV-dnMCU) were injected 16-18 weeks after injection with STZ (3x1011 genome copies in 100 μl). Experiments were carried out 5-6 months after STZ/HFD treatment and 4 weeks after AAV injection.
Growth protocol Type 2 diabetes (T2D) was induced in 12 week old C57BL/6 mice with a high fat diet (HFD, 60% calories from fat) (Envigo) and a single STZ injection of 75mg/kg (Fricovsky ES, Am. J. Phys. Reg. Int. Comp. Phys. 2013). Control groups were maintained on regular lab chow. T2D was defined 20 weeks after starting HFD with: fasting glucose levels >110 mg/dl, elevated glucose levels after glucose challenge, and elevated fed-state insulin (325 pmol/L vs. decreased insulin levels in T1D (32 pmol/L) and vs. control mice (100pmol/L)).
Extracted molecule total RNA
Extraction protocol Mouse hearts were lysed in Trizol (Thermo) and RNA was extracted by adding chloroform. RNA was then precipitated from the aqueous phase using isopropyl alcohol, washed with 70% ethanol and resuspended in diethyl pyrocarbonate (DEPC)-treated ddH20.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded Total RNA Library kit, ribosomal RNA depleted)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Basecalling, demultiplexing, and adapter trimming was performed using Illumina's bcl2fastq (v2.20.0.422)
RNA-seq reads were aligned to the GRCm38/mm10 assembly of the mouse genome using STAR (version 2.5.2a) with default parameters
Gene expression values were calculated across mouse GENCODE defined transcript exons using HOMERs analyzeRepeats.pl command. Raw read totals per gene were used to identify differentially expressed genes between each sample group using DESeq2 and normalized using DESeq2's rlog function to generate log2 gene expression values.
Genome_build: hg38
Supplementary_files_format_and_content: Table of normalized log2 counts (rlog) per gene and differential expression information (tab-delimited text) Columns: Gene Symbol, Ensembl ID, chr, start, end, strand, transcript length, annotation, sample1 rlog, sample2 rlog…, DESeq2 log2 fold change, DESeq2 p-value, DESeq2 adj. p-value for 3 separate pairwise comparisons, additional annotation columns.
 
Submission date Feb 13, 2020
Last update date Dec 15, 2022
Contact name Christopher Benner
E-mail(s) cbenner@ucsd.edu
Organization name University of California, San Diego (UCSD)
Department Medicine
Street address 9500 Gilman Dr. MC 0640
City La Jolla
State/province California
ZIP/Postal code 92093-0640
Country USA
 
Platform ID GPL19057
Series (1)
GSE145294 MCUb upregulation in the type 2 diabetic heart impacts cardiac function by altering mitochondrial metabolic fuel flux and the cardiac myocyte phosphoproteome
Relations
BioSample SAMN14101832
SRA SRX7724418

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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