Mouse colon, DSS day0 (steady state), 10x Visium (paper 5.5)
phalaena:sample:PA-S-5-5-colon-dss-day0
A steady-state (day-0, untreated) mouse colon section from the Parigi 2022 healing-intestine study, profiled as a 10x Visium spatial library, SRA run SRR14083626. We use it with its day-14 healing counterpart (PA-S-5-5-colon-dss-day14, SRR14083627) as a steady-state-vs-healing contrast on the same platform and protocol, and as part of the first colon slot in the validation corpus. The pipeline runs this sample in intake_qc mode: fastp read QC plus a unique R1 spot-barcode profile, no clustering and no Space Ranger. The section is head-subset to the first 35,000,000 read pairs, so composition-level reads of this sample are limited to the subset (see below).
- kind
- sample
- organism
- Mus musculus
- assay
- spatial transcriptomics, 10x_visium_spatial
- tissue
- colon
- instrument
- 10x Visium
- status
- reviewed
- ncbitaxon:10090
- insdc.sra:SRR14083626
- geo:GSE169749
- bioproject:PRJNA717789
View Mouse colon, DSS day0 (steady state), 10x Visium (paper 5.5) on the Phalaena Wiki