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| Status |
Public on Feb 15, 2024 |
| Title |
IPMN34, Geomx |
| Sample type |
SRA |
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| Source name |
High-grade IPMN
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| Organism |
Homo sapiens |
| Characteristics |
tissue: High-grade IPMN
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| 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
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Nanostring GeoMx
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| 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
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| Submission date |
Apr 14, 2023 |
| Last update date |
Feb 15, 2024 |
| Contact name |
Antonio Agostini |
| E-mail(s) |
agoan27@gmail.com
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| Organization name |
Università Cattolica del Sacro Cuore
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| Street address |
Largo Francesco Vito, 1
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| City |
Rome |
| ZIP/Postal code |
00168 |
| Country |
Italy |
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| 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 |
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| Relations |
| BioSample |
SAMN34191196 |
| SRA |
SRX19972609 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7177315_DSP-1001660014215-A-D04.dcc.gz |
71.2 Kb |
(ftp)(http) |
DCC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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