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Sample GSM7177346 Query DataSets for GSM7177346
Status Public on Feb 15, 2024
Title IPMN55, Geomx
Sample type SRA
 
Source name High-grade IPMN
Organism Homo sapiens
Characteristics tissue: High-grade IPMN
Extracted molecule total RNA
Extraction protocol 5μm sections from to TMA were used for library construction for spatial transcriptomics
Two IPMN TMA obtained from APGI were analyzed for spatial transcriptomics using GeoMX Human Whole Transcriptome Atlas (Nanostring, USA) following the provided protocol. TMAs were stained with GeoMX morphology kit to mark neoplastic cells (PanCK), and immune cells (CD45). After staining all TMA cores that showed signs of detachment and degradation, or contained few IPMN cells (< 100 nuclei) were discarded from the analysis. From the original set of 101 tissue cores from 61 patients, a total of 80 ROI from 46 patients were selected (multiple ROI from the same patient) for segmentation to isolate only the PanCK positive areas and exclude CD45 areas to obtain the specific transcriptome of IPMN cells
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description Nanostring GeoMx
Data processing Sequencing data was uploaded to the Illumina BaseSpace hub and processed with DRAGEN to obtain .dcc files
Assembly: GRCh38
Supplementary files format and content: tabular .dcc files
Library strategy: GEOmx Spatial Transcriptomics
 
Submission date Apr 14, 2023
Last update date Feb 15, 2024
Contact name Antonio Agostini
E-mail(s) agoan27@gmail.com
Organization name Università Cattolica del Sacro Cuore
Street address Largo Francesco Vito, 1
City Rome
ZIP/Postal code 00168
Country Italy
 
Platform ID GPL24676
Series (2)
GSE229752 Identification of spatially-resolved markers of malignant transformation in Intraductal Papillary Mucinous Neoplasms. [GeoMx]
GSE229878 Identification of novel spatially resolved markers of malignant transformation in Intraductal Papillary Mucinous Neoplasms
Relations
BioSample SAMN34191165
SRA SRX19972636

Supplementary file Size Download File type/resource
GSM7177346_DSP-1001660014215-A-F11.dcc.gz 73.8 Kb (ftp)(http) DCC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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