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Sample GSM7153005 Query DataSets for GSM7153005
Status Public on Aug 25, 2023
Title BCAA-free, 2W-TAC, rep2
Sample type SRA
 
Source name heart
Organism Mus musculus
Characteristics tissue: heart
strain: C57Bl/6J
Sex: male
age: 12-wk
treatment: BCAA-free diet, 2W-TAC surgery
Treatment protocol Mice were either maintained on a BCAA-control (all essential amino acids, incluing BCAA added in concnetration equivlarnt to those found in standard chow diets) or a BCAA-free diet, in which BCAA were completely elimnated). This was applied 4 days before the sham or TAC surgeries and continued throughout the survival period (2-wk after surgery).
Extracted molecule polyA RNA
Extraction protocol Trizol extraction of total RNA followed by polyA selection
1. mRNA enrichment, mRNA fragmentation, random priming. 2. First and second strand synthesis. 3. End repair, 5'phosphorylation, and dA-Tailing. 4. Adaptor ligation, PCR enrichment, and sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 2W-BFT2
2W-BFT-vs-BFS.csv
2W-BFT-vs-BCT.csv
Data processing Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Unique gene hit counts were calculated by using featuremCounts from the Subread package v.1.5.2.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between groups of samples was performed (as seen in the processed files). The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: mm10
Supplementary files format and content: The processed data are provided in csv files. The files include the gene ID, log2 fold change, padj, p value, the normalized reads for each each detectable gene in each of the samples being compared, and gene name. The log2 fold change are for the TAC/sham with either diet, or TAC(BCAA-free)/TAC(BCAA-control), or sham(BCAA-free)/sham(BCAA-contro). The samples in each file are identified by the designated library names.
 
Submission date Apr 06, 2023
Last update date Aug 25, 2023
Contact name Maha Abdellatif
E-mail(s) abdellma@rutgers.edu
Phone 9739721254
Organization name Rutgers University
Department Cell Biology and Molecular Medicine
Street address 185 S. Orange Ave., MSB
City Newark
State/province NJ
ZIP/Postal code 07103
Country USA
 
Platform ID GPL24247
Series (2)
GSE229128 The effect of a BCCA-free diet on 2W pressure overload-induced cardiac gene expression [BCAA-free-2W-TAC-RNA-Seq]
GSE229131 Lowering dietary BCAA reduces fibrosis, enhances mitochondrial respiration, and curbs cardiac hypertrophy, via regulating histone H3K23-propionylation
Relations
SRA SRX19899543
BioSample SAMN34104317

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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