ERC000011
ENA-CHECKLIST
2023-05-01T00:15:32Z
ENA-FIRST-PUBLIC
2023-05-01T00:15:32Z
ENA-LAST-UPDATE
SAMEA112303150
External Id
Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
INSDC center name
2023-05-01T00:15:32Z
INSDC first public
2023-05-01T00:15:32Z
INSDC last update
public
INSDC status
ERS14414081
SRA accession
E-MTAB-12468:Sample 1
Submitter Id
10
week
age
ArrayExpress
broker name
house mouse
common name
Protocols: Freshly isolated inguinal and mesenteric lymph nodes were collected from 10 weeks old mice and frozen in 2-Methybutane (Sigma, M32631) with liquid nitrogen and immediately embedded into frozen section media (FSC22 Leica, 3801480) for spatial transcriptomics. The tissue blocks were cut into 10-μm sections using cryostat and mounted on Visium gene expression slides (10x Genomics, PN-1000188). Following the commercial brochure of Visium gene expression kits (10x Genomics, PN-1000184) the tissue blocks were cut into 10-μm sections using cryostat and mounted on Visium gene expression slides (10x Genomics, PN-1000188). Sections on Visium Gene Expression slides were first fixed with pre-cooled methanol for 30 minutes and stained with DAPI, B220 and aSMA and imaged with confocal microscopy to visualize the fiducial frames of capture areas and cell compartmentalization in different sections. The optimal permeabilization time for murine lymph node sections was 15 minutes evaluated by 10x Genomics Visium tissue optimization kit (10x Genomics, PN-1000193) for in situ hybridization and reverse transcription. cDNA libraries were generated using Visium spatial gene expression 3′ library construction kit (10x Genomics, PN-1000190).
description
adult
developmental stage
C57BL/6N-Tg(Ccl19-Cre) x R26-EYFP
genotype
LN1
individual
Mus musculus
organism
Mus musculus
organism
lymph node
organism part
Mus musculus
scientific_name
female
sex
C57BL/6NJ
strain
Sample 1
title