characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-01-01T00:28:18Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-01-01T00:28:18Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA110377192
characteristics.characteristic: External Id
characteristics.text: Institute of Molecular Genetics of the Czech Academy of Sciences
characteristics.characteristic: INSDC center name
characteristics.text: 2023-01-01T00:28:18Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-01-01T00:28:18Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS12475388
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-11982:IEC_LP_6w
characteristics.characteristic: Submitter Id
characteristics.text: 6
characteristics.unit: week
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: mix of epithelial cell of small intestine and small intestinal lamina propria CD45+ cell
characteristics.characteristic: cell type
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: Mice were treated by peroral colonization with 50 microliters of cecal content from SFB monoassociated animals at 21 and 22 days of age or left untreated. Mice were euthanized by cervical dislocation, their small intestine was dissected. Epithelial cells were isolated from small intestines by serial incubation in HBSS + 3% FBS + 2mM EDTA followed by digestion in TrypLE Express enzyme. Intraepithelial cells were isolated in the same manner, but due to their lower frequency in the epithelial fraction they were enriched using 40%/80% percol gradient centrifugation. Lamina propria cells were isolated by the same protocol, but the epithelial fraction was discarded and remaining tissue was used further. This tissue was then minced, digested in collagenase D and DNAse I and immune cells were enriched using 40%/80% percol gradient centrifugation. Single cell suspension of intestinal epithelial cells, lamina propria cells or intraepithelial cells was sorted by flow cytometry as live, single cells. On the top of that, epithelial cells were sorted as CD45- EpCAM+, lamina propria cells and intraepithelial cells were sorted as CD45+. First-strand 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.
characteristics.characteristic: description
characteristics.text: juvenile
characteristics.characteristic: developmental stage
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: D
characteristics.characteristic: individual
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: small intestine
characteristics.characteristic: organism part
characteristics.text: 1
characteristics.characteristic: replicate
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: female
characteristics.characteristic: sex
characteristics.text: C57BL/6
characteristics.characteristic: strain
characteristics.text: IEC_LP_6w
characteristics.characteristic: title