Collections / A Spatially Resolved Transcriptome Landscape during Thyroid Cancer Progression

A Spatially Resolved Transcriptome Landscape during Thyroid Cancer Progression

Thyroid cancer ranks as the ninth most common cancer type in terms of incidence worldwide. Furthermore, the global incidence of thyroid cancer has been on the rise over the past decades.Spatial transcriptomics technology systematically profiles gene expression across tissue space by combing high-throughput RNA sequencing and imaging techniques. The applications of ST have revealed high-resolution spatial architecture and cellular crosstalk in many tumor types, advancing the discovery of new targets for diagnosis and therapy. However, the spatial architecture in thyroid cancer and the structural differences in the TME among papillary thyroid cancer (PTC), locally advanced thyroid cancer (LPTC), and Anaplastic thyroid carcinoma (ATC) have been little investigated. Herein , we applied ST and scRNA-seq data to reveal the spatial difference of TME in PTC, LPTC, and ATC samples.

Datasets16
Size~563 MB
AssayVisium
Samplehuman · thyroid gland
KindTime course
www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE250521 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse250521")
coll.ordered_artifacts.df()                 # the 16 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]

# …or load each straight into memory as a SpatialData object:
sdatas = {a.key: sd.read_zarr(a.cache()) for a in coll.ordered_artifacts.all()}
Member datasets · 16
Open in Vitessce
Visium
Human thyroid gland
GSM7980865
human thyroid gland thyroid gland carcinoma 51 MB 4,952 obs silver H&E
TechnologyVisium
Organismhuman
Tissuethyroid gland
Conditionthyroid gland carcinoma
Size51 MB
Obs4,952
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human thyroid gland
GSM7980870
human thyroid gland thyroid gland carcinoma 33 MB 4,633 obs silver H&E
TechnologyVisium
Organismhuman
Tissuethyroid gland
Conditionthyroid gland carcinoma
Size33 MB
Obs4,633
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human thyroid gland
GSM7980869
human thyroid gland thyroid gland carcinoma 33 MB 4,174 obs silver H&E
TechnologyVisium
Organismhuman
Tissuethyroid gland
Conditionthyroid gland carcinoma
Size33 MB
Obs4,174
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human thyroid gland
GSM7980875
human thyroid gland thyroid gland carcinoma 24 MB 2,594 obs silver H&E
TechnologyVisium
Organismhuman
Tissuethyroid gland
Conditionthyroid gland carcinoma
Size24 MB
Obs2,594
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human thyroid gland
GSM7980873
human thyroid gland thyroid gland carcinoma 22 MB 2,684 obs silver H&E
TechnologyVisium
Organismhuman
Tissuethyroid gland
Conditionthyroid gland carcinoma
Size22 MB
Obs2,684
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human thyroid gland
GSM7980871
human thyroid gland thyroid gland carcinoma 60 MB 4,737 obs silver H&E
TechnologyVisium
Organismhuman
Tissuethyroid gland
Conditionthyroid gland carcinoma
Size60 MB
Obs4,737
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human thyroid gland
GSM7980867
human thyroid gland thyroid gland carcinoma 43 MB 4,748 obs silver H&E
TechnologyVisium
Organismhuman
Tissuethyroid gland
Conditionthyroid gland carcinoma
Size43 MB
Obs4,748
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human thyroid gland
GSM7980864
human thyroid gland thyroid gland carcinoma 20 MB 2,270 obs silver H&E
TechnologyVisium
Organismhuman
Tissuethyroid gland
Conditionthyroid gland carcinoma
Size20 MB
Obs2,270
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human thyroid gland
GSM7980872
human thyroid gland thyroid gland carcinoma 46 MB 4,722 obs silver H&E
TechnologyVisium
Organismhuman
Tissuethyroid gland
Conditionthyroid gland carcinoma
Size46 MB
Obs4,722
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human thyroid gland
GSM7980863
human thyroid gland 33 MB 3,030 obs silver H&E
TechnologyVisium
Organismhuman
Tissuethyroid gland
Size33 MB
Obs3,030
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human thyroid gland
GSM7980862
human thyroid gland 41 MB 4,547 obs silver H&E
TechnologyVisium
Organismhuman
Tissuethyroid gland
Size41 MB
Obs4,547
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human thyroid gland
GSM7980868
human thyroid gland thyroid gland carcinoma 21 MB 1,520 obs silver H&E
TechnologyVisium
Organismhuman
Tissuethyroid gland
Conditionthyroid gland carcinoma
Size21 MB
Obs1,520
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human thyroid gland
GSM7980874
human thyroid gland thyroid gland carcinoma 27 MB 1,622 obs silver H&E
TechnologyVisium
Organismhuman
Tissuethyroid gland
Conditionthyroid gland carcinoma
Size27 MB
Obs1,622
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human thyroid gland
GSM7980866
human thyroid gland thyroid gland carcinoma 47 MB 4,524 obs silver H&E
TechnologyVisium
Organismhuman
Tissuethyroid gland
Conditionthyroid gland carcinoma
Size47 MB
Obs4,524
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human thyroid gland
GSM7980860
human thyroid gland 23 MB 3,401 obs silver H&E
TechnologyVisium
Organismhuman
Tissuethyroid gland
Size23 MB
Obs3,401
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human thyroid gland
GSM7980861
human thyroid gland 37 MB 3,839 obs silver H&E
TechnologyVisium
Organismhuman
Tissuethyroid gland
Size37 MB
Obs3,839
silver H&E Open in Vitessce

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