Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0

Spatially resolved transcriptomic profiling: an experimental comparison of GeoMx Digital Spatial Profiling and Visium CytAssist spatial transcriptomics in three cancer types (GeoMx)


ABSTRACT: We performed Visium CytAssist (10X), GeoMx DSP (Nanostring) and Chromium Flex (10X Genomics) full transcriptome profiling on Breast Cancer (BC), Lung Cancer (LC) and diffuse large B cell lymphoma (DLBCL) samples from archival FFPE blocks. We explore the data quality across blocks with different storage times and DV200 values for all the three methods. We compared the cell type signature purity between ST methods Visium and GeoMx by utilising pathology annotations and scRNAseq. For the Visium and Chromium methods with a large number of data points we explored the heterogeneity between tissues. Finally, we demonstrate the discovery of patient-specific tumor-TME interactions across all three methods.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Senbai Kang 

PROVIDER: E-MTAB-14566 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

Similar Datasets

2024-11-01 | E-MTAB-14560 | biostudies-arrayexpress
2020-11-16 | PXD020362 | Pride
2017-10-05 | PXD005834 | Pride
2024-08-04 | PXD052574 | Pride
2019-06-06 | PXD014142 | Pride
2024-05-28 | E-MTAB-14121 | biostudies-arrayexpress
2018-10-26 | PXD005650 | Pride
2014-10-30 | E-GEOD-62182 | biostudies-arrayexpress
2022-01-27 | E-MTAB-11265 | biostudies-arrayexpress
2010-03-18 | E-GEOD-20935 | biostudies-arrayexpress