Mouse colon, DSS day14 (mucosal healing), 10x Visium (paper 5.5)
phalaena:sample:PA-S-5-5-colon-dss-day14
A healing (day-14) mouse colon section from the Parigi 2022 healing-intestine study, profiled as a 10x Visium spatial library, SRA run SRR14083627. The day-14 timepoint is colon collected after 7 days of DSS in drinking water followed by 7 days of recovery, the mucosal-healing condition of the study. We use it with its day-0 steady-state counterpart (PA-S-5-5-colon-dss-day0, SRR14083626) as a steady-state-vs-healing contrast on the same platform and protocol. 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:SRR14083627
- geo:GSE169749
- bioproject:PRJNA717789
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