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| Status |
Public on Aug 31, 2024 |
| Title |
Type 2 Diabetes Specific Spatial Differential Gene Expression in Pancreas Visium Data |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
Understanding the spatial distribution of gene expression in the pancreas could provide new insights into its function and islet biology. Visium spatial gene expression is a powerful tool for quantifying gene expression of cells within their spatial context. We describe the generation and analysis of spatial transcriptomics data from six pancreas samples from healthy donors. Our analysis revealed high expression of INS within islets. However, we also identified a bleed of highly abundant islet genes (e.g., INS, GCG) into surrounding tissue areas. Through computational analyses, we successfully corrected for this bleed. We then identify genes which are spatially differentially expressed in the Type 2 Diabetes samples. We provide these data for researchers to study the organization of the pancreas and islets.
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| Overall design |
human pancreatic tissue flash frozen with isopentane; tissue sections prepared and processed with the 10X Genomics Visium Spatial Gene Expression Reagent kit
>>>Raw data were deposited in dbGaP under phs001188.v3.p1 due to patient privacy concerns.<<<<
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| Contributor(s) |
Bonnycastle LL, Erdos MR, Grenko C, Weiss Z, Robertson C, Narisu N, Taylor L, Collins FS |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Apr 18, 2024 |
| Last update date |
Aug 31, 2024 |
| Contact name |
Neelam Sinha |
| E-mail(s) |
neelam.sinha@nih.gov
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| Phone |
2096008408
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| Organization name |
NIH
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| Department |
NHGRI
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| Lab |
Dr. Collins lab
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| Street address |
4998, BATTERY LN, APT 206
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20814 |
| Country |
USA |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA1101984 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE264331_RAW.tar |
22.3 Gb |
(http)(custom) |
TAR (of H5, JPG, TIFF) |
| Raw data not provided for this record |
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