|
| Status |
Public on Sep 07, 2023 |
| Title |
Patient LIMET139 multiplexed fluorescent in situ RNA hybridization ROI B2 |
| Sample type |
other |
| |
|
| Source name |
Primary tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Primary tumor
disease state: PDAC
individual: Patient LIMET139
|
| Extracted molecule |
other |
| Extraction protocol |
n/a
|
| Label |
n/a
|
| Label protocol |
n/a
|
| |
|
| Hybridization protocol |
Briefly, 10-µm PDAC tissue sections were hybridized at 37°C for 24 hours with oligonucleotides probes specific for the selected target genes, designed using Resolve’s proprietary algorithm.
|
| Scan protocol |
Probe binding was revealed with fluorescent tags in a multi-step automated imaging process, repeating color development, imaging and decolorization for a total of 8 cycles on a Zeiss Celldiscoverer 7 instrument, using a 50x water immersion objective.
|
| Description |
Raw data files include tab-separated values files containing x-y-z location for each transcript (txt format) and staining images of DAPI and KRT19 (tiff format).Processed data include output from segmentation with Baysor.
|
| Data processing |
We segmented cell nuclei in the DAPI image with Cellpose (v. 2.2) using the pre-trained nuclei model, with automated estimation of diameter parameter. Subsequently, cells were segmented on transcript coordinates with Baysor (v. 0.5.0) using DAPI segments as prior.
|
| |
|
| Submission date |
Jul 20, 2023 |
| Last update date |
Sep 07, 2023 |
| Contact name |
Renato Ostuni |
| Organization name |
San Raffaele Telethon Institute for Gene Therapy
|
| Street address |
Via Olgettina 58
|
| City |
Milano |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL33597 |
| Series (2) |
| GSE217847 |
IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer |
| GSE237846 |
IL-1b+ tumor-associated macrophages fuel pathogenic inflammation in pancreatic cancer - Molecular Cartography of human PDAC samples |
|
