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Status |
Public on Jan 30, 2023 |
Title |
T2DM_Mac_D3_rHDL_rep3_S44 |
Sample type |
SRA |
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Source name |
Gastrocnemius muscle
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Organism |
Mus musculus |
Characteristics |
strain: IGF-II/LDLR-/-ApoB100/100 , with C57BL/6J background treatment: reconstituted HDL (rHDL)-ApoA-I cell type: Ischemic Macrophages time point: 3 days post femoral artery ligation replicate: 3 disease state: Diabetic
|
Treatment protocol |
Unilateral hindlimb ischemia was induced by ligating femoral artery proximal to the bifurcation of superficial and deep femoral artery in control and type 2 diabetic mice. Mice were were administered with reconstituted ApoA-I nanoparticles with phosphatidyl serine core (rHDL) intravenously starting 2 days post-HLI with doses every 2 days until scarification with Saline injections serving as controls. Ishcemic muscle macrophages and endothelial cells were FACS sorted at 3 and 7 days after ischemia induction.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated from FACS sorted ECs and Macrophagess from ischemic muscles using Arcturus PicoPure RNA isolation Kit (Applied Biosystems) Lexogen QuantSeq 3’mRNA-Seq Library Prep Kit-FWD (Lexogen, Vienna, Austria) was used to prepare 3′ RNA-Seq libraries. The double stranded DNA concentrations were quantified using a 5200 Fragment Analyzer (Part # M5310AA, Agilent Technologies), which gave similar concentrations for each sample that ranged from 1.7 to 4.3 ng/ μL. The molar concentration of cDNA molecules in the individual libraries was calculated from the DNA concentration and the region average size. Aliquots containing an equal number of nmoles of molecules from each library were pooled to give a pooled library with a concentration of 10 nM molecules. After library preparation, libraries were pooled and sequenced using single-end sequencing with 75 bp reads on an Illumina NextSeq500 instrument (Illumina, San Diego, CA).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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|
Data processing |
RNA-Seq reads were first trimmed to remove low-quality bases, poly(A) and Illumina adapter using cutadapt (version 2.8). Subsequently, the reads were processed using the nf-core RNA-Seq pipeline (version 1.4.2) with the mm10 mouse genome and the STAR aligner for read mapping and the Ensembl GRCm38 release 93 gene annotations for counting reads in transcripts. The following gene biotypes were retained in the gene expression matrix: protein coding, lincRNA and antisense. Genome_build: mm10 Supplementary_files_format_and_content: raw count matrix
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|
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Submission date |
Feb 24, 2022 |
Last update date |
Jan 30, 2023 |
Contact name |
Tiit Örd |
E-mail(s) |
tiit.ord@uef.fi
|
Organization name |
A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland
|
Lab |
Cardiovascular Genomics (Minna Kaikkonen)
|
Street address |
Neulaniementie 2
|
City |
Kuopio |
ZIP/Postal code |
70211 |
Country |
Finland |
|
|
Platform ID |
GPL19057 |
Series (1) |
GSE197392 |
ApoA-I nanotherapy rescues inadequate post-ischemic vascular adaptation in diabetic mice by modulating macrophage phenotype |
|
Relations |
BioSample |
SAMN26232537 |
SRA |
SRX14279332 |