Intermittent childhood hyperlipidaemia alters resident arterial macro... - SRA

ERX10475593: Intermittent childhood hyperlipidaemia alters resident arterial macrophages and accelerates atherosclerosis
1 ILLUMINA (Illumina HiSeq 4000) run: 51M spots, 2.5G bases, 1.1Gb downloads

Design: Intermittent childhood hyperlipidaemia alters resident arterial macrophages and accelerates atherosclerosis

Submitted by: EBI (European Bioinformatics Institute)

Study: Intermittent childhood hyperlipidaemia alters resident arterial macrophages and accelerates atherosclerosis

PRJEB60780 • ERP145841 • All experiments • All runs

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Mice deficient in the LDL receptor (LDLR KO mice) fed with high fat diet (HFD) feeding have been widely used as a model to mimic human atherosclerosis. RNA-seq using aortic macrophages to investigate the effects of aortic macrophages on the plaque size progression. LDLR KO mice, 6-8 weeks old, were used, and fed with either an alternative HFD or a regular HFD. After aorta macrophages were isolated, RNeasy Mini Kit (Qiagen) was used to isolate mRNA. Single end (50bp), unstranded, SMART-Seq v4 plus nextera (SMART-Seq v4 Ultra Low Input RNA Kit (Takara) ). The RNA-seq libraries were prepared with SMART-Seq v4 Ultra Low Input RNA Kit (Takara).

Sample: Sample 9

SAMEA112797989 • ERS14805535 • All experiments • All runs

Organism: Mus musculus

Library:

Name: Sample 9_s

Instrument: Illumina HiSeq 4000

Strategy: RNA-Seq

Source: GENOMIC

Selection: RANDOM

Layout: SINGLE

Construction protocol: Aortas were harvested and cleaned of contaminated tissues. Aortas were subjected to enzymatic digestion method and single cell suspensions of aortic cells were prepared. Cell suspensions were incubated with Zombie Aqua™ Fixable Viability Kit (BioLegend) and then cells were stained with fluorescently labelled anti-mouse antibodies against CD45, CD11b and CD64. Aortic macrophages were identified as CD45+CD11b+CD64+. Animals were perfused with cold PBS to remove any trace of blood. Aortas were harvested and cleaned of contaminated tissues under a dissection microscope 16 wks mouse high fat diet. Align to GRCm39 reference genome using star (version 2.6.1d) RNA extraction and residual DNA removal upon DNase digestion was performed with the RNeasy mini kit (Qiagen) according to the manufacturer's instructions. After quality check with Agilent Bioanalyser 2100 system, total RNA was made into sequencing libraries. Takara's SMART-Seq v4 Ultra Low Input RNA Kit.

Experiment attributes:

Experimental Factor: diet: cWD

Runs: 1 run, 51M spots, 2.5G bases, 1.1Gb

Run	# of Spots	# of Bases	Size	Published
ERR11039748	50,984,442	2.5G	1.1Gb	2024-08-01

ID:: 34520805

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