2025-07-18
ENA first public
ERC000011
ENA-CHECKLIST
Max Planck Institute of Immunobiology and Epigenetics (MPI-IE)
INSDC center name
public
INSDC status
ERS22551576
SRA accession
E-MTAB-13580_3:FB_4-oxo_3
Submitter Id
12
week
age
ArrayExpress
broker name
monocytes (CD11b+)
cell_type
not collected
collection date
house mouse
common name
Protocols: In Fgd5CreERT2 mice, LAD was performed, followed by a 2-day treatment with either vehicle (DMSO) or 4-oxo-RA. On day 3 post-MI, hearts were extracted, and dTomato-positive and dTomato-negative myeloid cells (CD11b pos) were isolated from the myocardium. Cardiac myeloid cells were sorted in 2% BSA in PBS in 1 biological replicate. n.a. Sorted cells in PBS supplemented with 2% BSA were pelleted at 300g for 5 min at 4 °C and washed once in ice-cold PBS containing 0.5% BSA. Cells were resuspended in PBS with 0.5% BSA to a maximum cell concentration of 390 cells/_l and placed on ice. Cell viability was assessed by trypan blue staining. A cell suspension aliquot (2 _l) was diluted 1:2 in 0.4% trypan blue solution, incubated for 2 minutes on a microscope slide and analyzed under a microscope. All samples for scRNA-seq analysis showed more than 90% viable cells. Single cell RNA-sequencing was performed on the 10X Genomics platform using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 dual index (10x Genomics, PN-1000268) following the manufacturer's instructions. A total of 43 _l of cell suspension was loaded onto a chip G according to the manufacturer’s instructions, aiming for a targeted cell recovery of up to 10,000 cells. PCR cycles for cDNA and final library generation were adjusted according to the target cell recoveries.  The quality of the obtained cDNA and final libraries was assessed by capillary electrophoresis (Fragment analyzer, HS NGS Fragment Kit, Agilent).
description
adult
developmental stage
Fgd5-CreERT2
genotype
not collected
geographic location (country and/or sea)
Mouse 3
individual
not applicable
isolate
Mus musculus
organism
Mus musculus
organism
heart
organism part
Mus musculus
scientific_name
female
sex
Myocardial infarction (LAD)
stimulus
FB_4-oxo_3
title