Collections / COLON MAP: Colon Molecular Atlas Project

COLON MAP: Colon Molecular Atlas Project

Datasets41
Size~103 GB
AssayVisium
Samplehuman · intestine
KindComparison
10.1016/j.cell.2023.11.006 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="doi-10.1016/j.cell.2023.11.006")
coll.ordered_artifacts.df()                 # the 41 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()}
About the study

Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors.

Colorectal cancer exhibits dynamic cellular and genetic heterogeneity during progression from precursor lesions toward malignancy. Analysis of spatial multi-omic data from 31 human colorectal specimens enabled phylogeographic mapping of tumor evolution that revealed individualized progression trajectories and accompanying microenvironmental and clonal alterations. Phylogeographic mapping ordered genetic events, classified tumors by their evolutionary dynamics, and placed clonal regions along global pseudotemporal progression trajectories encompassing the chromosomal instability (CIN+) and hypermutated (HM) pathways. Integrated single-cell and spatial transcriptomic data revealed recurring epithelial programs and infiltrating immune states along progression pseudotime. We discovered an immune exclusion signature (IEX), consisting of extracellular matrix regulators DDR1, TGFBI, PAK4, and DPEP1, that charts with CIN+ tumor progression, is associated with reduced cytotoxic cell infiltration, and shows prognostic value in independent cohorts. This spatial multi-omic atlas provides insights into colorectal tumor-microenvironment co-evolution, serving as a resource for stratification and targeted treatments.

Member datasets · 41
Open in Vitessce
Visium
Human intestine
MISC65
human intestine colon adenocarcinoma 2.1 GB 3,261 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size2.1 GB
Obs3,261
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC56
human intestine colon adenocarcinoma 2.9 GB 3,395 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size2.9 GB
Obs3,395
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC54
human intestine colorectal adenoma 1.7 GB 668 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolorectal adenoma
Size1.7 GB
Obs668
Magnification40x · 0.275 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC70
human intestine colon adenocarcinoma 2.6 GB 3,934 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size2.6 GB
Obs3,934
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC51
human intestine colon adenocarcinoma 2.4 GB 3,076 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size2.4 GB
Obs3,076
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC63
human intestine colon adenocarcinoma 3.1 GB 3,467 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size3.1 GB
Obs3,467
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC33
human intestine colon adenocarcinoma 1.6 GB 3,385 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size1.6 GB
Obs3,385
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC38
human intestine colon adenocarcinoma 978 MB 1,727 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size978 MB
Obs1,727
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC66
human intestine colon adenocarcinoma 2.9 GB 3,970 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size2.9 GB
Obs3,970
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC50
human intestine colon adenocarcinoma 2.8 GB 4,297 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size2.8 GB
Obs4,297
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC64
human intestine colon adenocarcinoma 2.0 GB 2,533 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size2.0 GB
Obs2,533
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC49
human intestine colon adenocarcinoma 4.1 GB 4,624 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size4.1 GB
Obs4,624
Magnification40x · 0.277 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC35
human intestine colon adenocarcinoma 2.3 GB 3,578 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size2.3 GB
Obs3,578
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC58
human intestine colon adenocarcinoma 1.7 GB 1,165 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size1.7 GB
Obs1,165
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC72
human intestine colon adenocarcinoma 3.0 GB 4,369 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size3.0 GB
Obs4,369
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC67
human intestine colon adenocarcinoma 2.2 GB 2,551 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size2.2 GB
Obs2,551
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC39
human intestine colon adenocarcinoma 2.5 GB 4,078 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size2.5 GB
Obs4,078
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC44
human intestine colon adenocarcinoma 1.6 GB 932 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size1.6 GB
Obs932
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC61
human intestine colorectal adenoma 2.2 GB 2,047 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolorectal adenoma
Size2.2 GB
Obs2,047
Magnification40x · 0.277 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC42
human intestine colon adenocarcinoma 1.6 GB 659 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size1.6 GB
Obs659
Magnification40x · 0.274 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC47
human intestine colon adenocarcinoma 3.9 GB 4,818 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size3.9 GB
Obs4,818
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC36
human intestine colon adenocarcinoma 2.3 GB 3,502 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size2.3 GB
Obs3,502
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC57
human intestine colon adenocarcinoma 1.7 GB 989 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size1.7 GB
Obs989
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC45
human intestine colon adenocarcinoma 4.5 GB 4,118 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size4.5 GB
Obs4,118
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC68
human intestine colon adenocarcinoma 2.8 GB 2,708 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size2.8 GB
Obs2,708
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC53
human intestine colorectal adenoma 1.8 GB 818 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolorectal adenoma
Size1.8 GB
Obs818
Magnification40x · 0.277 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC41
human intestine colon adenocarcinoma 3.9 GB 3,708 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size3.9 GB
Obs3,708
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC52
human intestine colorectal adenoma 1.7 GB 229 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolorectal adenoma
Size1.7 GB
Obs229
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC46
human intestine colon adenocarcinoma 4.3 GB 4,511 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size4.3 GB
Obs4,511
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC55
human intestine colorectal adenoma 1.7 GB 863 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolorectal adenoma
Size1.7 GB
Obs863
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC48
human intestine colon adenocarcinoma 2.8 GB 3,577 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size2.8 GB
Obs3,577
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC62
human intestine colon adenocarcinoma 2.8 GB 4,132 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size2.8 GB
Obs4,132
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC69
human intestine colon adenocarcinoma 3.0 GB 3,634 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size3.0 GB
Obs3,634
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC71
human intestine colon adenocarcinoma 3.6 GB 2,997 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size3.6 GB
Obs2,997
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC37
human intestine colon adenocarcinoma 1.5 GB 3,636 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size1.5 GB
Obs3,636
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC34
human intestine colon adenocarcinoma 2.0 GB 3,731 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size2.0 GB
Obs3,731
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC59
human intestine colorectal adenoma 3.0 GB 1,312 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolorectal adenoma
Size3.0 GB
Obs1,312
Magnification40x · 0.275 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC43
human intestine colon adenocarcinoma 1.7 GB 1,186 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size1.7 GB
Obs1,186
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC40
human intestine colon adenocarcinoma 2.4 GB 4,116 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size2.4 GB
Obs4,116
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC60
human intestine colorectal adenoma 2.1 GB 1,014 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolorectal adenoma
Size2.1 GB
Obs1,014
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human intestine
MISC73
human intestine colon adenocarcinoma 3.3 GB 3,901 obs silver H&E
TechnologyVisium
Organismhuman
Tissueintestine
Conditioncolon adenocarcinoma
Size3.3 GB
Obs3,901
Magnification40x · 0.276 µm/px
silver H&E Open in Vitessce

Cite this collection

doi.org/10.1016/j.cell.2023.11.006 ↗
BibTeX 
@article{Heiser_2023,
  title = {Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors},
  volume = {186},
  ISSN = {0092-8674},
  url = {http://dx.doi.org/10.1016/j.cell.2023.11.006},
  DOI = {10.1016/j.cell.2023.11.006},
  number = {25},
  journal = {Cell},
  publisher = {Elsevier BV},
  author = {Heiser, Cody N. and Simmons, Alan J. and Revetta, Frank and McKinley, Eliot T. and Ramirez-Solano, Marisol A. and Wang, Jiawei and Kaur, Harsimran and Shao, Justin and Ayers, Gregory D. and Wang, Yu and Glass, Sarah E. and Tasneem, Naila and Chen, Zhengyi and Qin, Yan and Kim, William and Rolong, Andrea and Chen, Bob and Vega, Paige N. and Drewes, Julia L. and Markham, Nicholas O. and Saleh, Nabil and Nikolos, Fotis and Vandekar, Simon and Jones, Angela L. and Washington, M. Kay and Roland, Joseph T. and Chan, Keith S. and Schürpf, Thomas and Sears, Cynthia L. and Liu, Qi and Shrubsole, Martha J. and Coffey, Robert J. and Lau, Ken S.},
  year = {2023},
  month = Dec,
  pages = {5620–5637.e16}
}