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Sample GSM8291000

Query DataSets for GSM8291000

Status

Public on Nov 28, 2024

Title

Classical-PanCK-B01

Sample type

SRA

Source name

Epithelial_cells

Organism

Homo sapiens

Characteristics

nec subtype: Classical
cell subtype: PanCK+
cluster: PanPre_1
cell type: Epithelial_cells
patient: 2

Extracted molecule

total RNA

Extraction protocol

Archived formalin-fixed, paraffin-embedded ileal tissue blocks were sectioned (5 µm) and stained with fluorescent antibody morphological markers, bound to UV-photocleavable oligos, for epithelial (panCK)- and immune (CD45)-rich regions.
Spatial transcriptome sequencing libraries were prepared for NanoString Digital Spatial Profiling using the human GeoMx® Whole Transcriptome Atlas kit and reagents, according to manufacturer's instructions.

Library strategy

OTHER

Library source

transcriptomic

Library selection

other

Instrument model

Illumina HiSeq 2500

Description

Formalin-fixed, paraffin-embedded spatial transcriptome sequencing
DSP.1006550110648.B.B01

Data processing

DSS files with raw count data were imported into R, QC filtered according to Nanostring protocols, and normalized using GeomxTools package from Bioconductor.
Normalized data were coerced into a Seurat object and standard subsequent analyses, comprising SCTransform data integration over all patients, PCA/UMAP/tSNE dimensionality reduction and clustering, was performed using the integrated pipeline of Seurat R package.
Mixed cell deconvolution in each ROI, estimating ROI dominant cell type identity, was performed using the SpatialDecon R Package and both primary and granular matrices derived from cell profiles defined in the Human Cell Atlas (HCA) intestine dataset. Relative percentage distribution and enrichment of cell types across clusters, disease type and Pan-CK/CD45 condition was studied with Correspondence Analysis tools.
Using reverse deconvolution, genes with cell-type abundance-independent expression variation were filtered for downstream differential analysis. Identification of conserved cell type markers within each cluster and differential expression analysis between ROI conditions and NEC subtypes relied on Seurat function FindMarkers.
Ingenuity Pathway Analysis (IPA, QIAGEN, Redwood City CA) was used to identify and interactively explore significantly altered pathways, functional sets and gene networks, enriched among the set of DE genes.
Assembly: GRCh38 (hg38)
Supplementary files format and content: countsSCT.txt.gz: tab delimited text file with raw counts per gene per sample
Supplementary files format and content: AllDataHumanProtein.xlsx : Excel file containing raw and normalized concentration values for 77 proteins for a subset of patients (n = 2 cardiac NEC, n = 2 classical NEC, ~6 ROIs/patient) used to validate transcriptomics
Supplementary files format and content: CS16_1492_1D_CS18_190_1C.png : Hi-res images of cardiac (CS16-1492-1D) and classical (CS18-190-1C) NEC tissue immunofluorescent morphological staining and ROI selection
Supplementary files format and content: CS17_128_3B_CS19_1149_1B.png : Hi-res images of cardiac (CS17-128-3B) and classical (CS19-1149-1B) NEC tissue immunofluorescent morphological staining and ROI selection
Supplementary files format and content: CS13_1240_CS15_843.png : Hi-res images of classical (CS13-1240 and CS15-843) NEC tissue immunofluorescent morphological staining and ROI selection
Supplementary files format and content: CS15_1579_CS15_1962.png : Hi-res image of classical (CS15-1579) NEC tissue immunofluorescent morphological staining and ROI selection
Library strategy: Spatial Transcriptomics

Submission date

May 28, 2024

Last update date

Nov 28, 2024

Contact name

Jonathan Wren

E-mail(s)

[email protected]

Phone

(405) 271-6989

Organization name

OMRF