2025-04-01
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA115169985
External Id
Institute of Molecular Genetics of the Czech Academy of Sciences
INSDC center name
2024-01-31T22:32:30Z
INSDC last update
public
INSDC status
ERS18056498
SRA accession
E-MTAB-13752:Colon_tumor
Submitter Id
15
week
age
ArrayExpress
broker name
colon adenoma
cell_type
not collected
collection date
house mouse
common name
Protocols: Adult littermates of the Apc-min Rosa26-tdTomato Defa6-iCre mouse strain were sacrificed by cervical dislocation. In these mice developing multiple intestinal tumors, cells expressing Defa6 producing constitutively active Cre recombinase are marked by endogenous expression of the red fluorescent protein tdTomato. Adenomas from the colon of these mice were isolated, and a suspension of single cells was prepared by dispase and collagenase cleavage. Cells were stained with the following antibodies: Hoechst33358, anti-CD45-PacificBlue, anti-CD31-PacificBlue, anti-EpCAM-FITC. Using fluorescence-activated cell sorting (FACS), we isolated Hoechst-/CD45-/CD31-/EpCAM+ cells, i.e. all epithelial colon tumor cells, and Hoechst-/CD45-/CD31-/EpCAM+/tdTomato+ cells, i.e. Defa6+ cells from colon tumor. Defa6+ cells were mixed from two animals to obtain a sufficient number of cells. cDNA was extracted from cell suspension during library preparation routine using Chromium next gem single-cell 3′ reagent kit (version 3.1). Single-cell RNA-seq libraries were prepared using Chromium controller instrument and Chromium Next Gem single-cell 3’ reagent kit version 3.1 (both 10X Genomics, Pleasanton, CA, USA) according to the manufacturer’s protocol targeting 4000 cells per sample.
description
adult
developmental stage
Apc heterogous mutation
genotype
not collected
geographic location (country and/or sea)
A
individual
not applicable
isolate
Mus musculus
organism
Mus musculus
organism
colon
organism part
Mus musculus
scientific_name
male
sex
C57BL/6
strain
Colon_tumor
title