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Reference profile for couse colon #19

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Reference profile for couse colon #19

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c49cfca
add RData file with profile_matrix and cellGroups objects
dan11mcguire Sep 14, 2023
e988127
update with sheet for colon celltypes
dan11mcguire Sep 14, 2023
623a322
update with row for colon metadata
dan11mcguire Sep 14, 2023
a7bb1fb
upate with RData object including cellGroups and profile_matrix
dan11mcguire Sep 14, 2023
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Binary file added Mouse/Adult/Colon_SCP2038.RData
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81 changes: 41 additions & 40 deletions Mouse/Mouse_datasets_metadata.csv
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Profile Matrix,Tissue,Species,Strain,Age,Age Group,URL,Citation
MCA,Bladder,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,BoneMarrow,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,BoneMarrow_cKit,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
Profile Matrix,Tissue,Species,Strain,Age,Age Group,URL,Citation
MCA,Bladder,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,BoneMarrow,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,BoneMarrow_cKit,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
AllenBrainAtlas,Brain,Mouse,"C57BL/6J, Nkx2.1-CreERT2;Ai14",8 weeks,Adult,"https://www.biorxiv.org/content/10.1101/2020.03.30.015214v1.full#F1
https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-10x","Yao, Z. et al. A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation. bioRxiv 2020.03.30.015214 (2020) doi:10.1101/2020.03.30.015214."
MCA,Brain,Mouse,"C57BL/6","6-10 weeks",Adult,"https://pubmed.ncbi.nlm.nih.gov/29474909/","Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
ImmGen,ImmuneAtlas,Mouse,"C57BL/6, B6.Rorc.tm2Litt",5-6 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/30686579/,"Yoshida, H. et al. The cis-Regulatory Atlas of the Mouse Immune System. Cell 176, 897-912.e20 (2019)."
ImmGen_cellFamily,ImmuneAtlas,Mouse,"C57BL/6, B6.Rorc.tm2Litt",5-6 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/30686579/,"Yoshida, H. et al. The cis-Regulatory Atlas of the Mouse Immune System. Cell 176, 897-912.e20 (2019)."
MCA,Kidney,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Liver,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Lung,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,MammaryGland_Involution,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,MammaryGland_Lactation,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,MammaryGland_Pregnancy,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,MammaryGland_Virgin,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Muscle,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Ovary,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Pancreas,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,PeripheralBlood,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Placenta,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Prostate,Mouse,C57BL/6,8-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,SmallIntestine,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Spleen,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Stomach,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Testis,Mouse,C57BL/6,8-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Thymus,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Uterus,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,EmbryonicMesenchyme,Mouse,C57BL/6,14.5 days,Fetal/E14.5,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-10x","Yao, Z. et al. A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation. bioRxiv 2020.03.30.015214 (2020) doi:10.1101/2020.03.30.015214."
MCA,Brain,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
ImmGen,ImmuneAtlas,Mouse,"C57BL/6, B6.Rorc.tm2Litt",5-6 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/30686579/,"Yoshida, H. et al. The cis-Regulatory Atlas of the Mouse Immune System. Cell 176, 897-912.e20 (2019)."
ImmGen_cellFamily,ImmuneAtlas,Mouse,"C57BL/6, B6.Rorc.tm2Litt",5-6 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/30686579/,"Yoshida, H. et al. The cis-Regulatory Atlas of the Mouse Immune System. Cell 176, 897-912.e20 (2019)."
MCA,Kidney,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Liver,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Lung,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,MammaryGland_Involution,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,MammaryGland_Lactation,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,MammaryGland_Pregnancy,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,MammaryGland_Virgin,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Muscle,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Ovary,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Pancreas,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,PeripheralBlood,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Placenta,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Prostate,Mouse,C57BL/6,8-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,SmallIntestine,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Spleen,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Stomach,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Testis,Mouse,C57BL/6,8-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Thymus,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Uterus,Mouse,C57BL/6,6-10 weeks,Adult,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,EmbryonicMesenchyme,Mouse,C57BL/6,14.5 days,Fetal/E14.5,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MOCA,FetalAtlas,Mouse,C57BL/6,9.5 and 13.5 days,Fetal/E9.5-13.5,"https://doi.org/10.1038/s41586-019-0969-x
https://oncoscape.v3.sttrcancer.org/atlas.gs.washington.edu.mouse.rna/downloads","Cao, J. et al. The single cell transcriptional landscape of mammalian organogenesis. Nature 566, 496–502 (2019)."
MCA,Brain,Mouse,C57BL/6,14.5 days,Fetal/E14.5,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Intestine,Mouse,C57BL/6,14.5 days,Fetal/E14.5,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Liver,Mouse,C57BL/6,14.5 days,Fetal/E14.5,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Lung,Mouse,C57BL/6,14.5 days,Fetal/E14.5,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Stomach,Mouse,C57BL/6,14.5 days,Fetal/E14.5,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Calvaria,Mouse,C57BL/6,1 day,Neonatal,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Heart,Mouse,C57BL/6,1 day,Neonatal,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Muscle,Mouse,C57BL/6,1 day,Neonatal,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Pancreas,Mouse,C57BL/6,1 day,Neonatal,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Rib,Mouse,C57BL/6,1 day,Neonatal,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Skin,Mouse,C57BL/6,1 day,Neonatal,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
https://oncoscape.v3.sttrcancer.org/atlas.gs.washington.edu.mouse.rna/downloads","Cao, J. et al. The single cell transcriptional landscape of mammalian organogenesis. Nature 566, 496–502 (2019)."
MCA,Brain,Mouse,C57BL/6,14.5 days,Fetal/E14.5,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Intestine,Mouse,C57BL/6,14.5 days,Fetal/E14.5,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Liver,Mouse,C57BL/6,14.5 days,Fetal/E14.5,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Lung,Mouse,C57BL/6,14.5 days,Fetal/E14.5,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Stomach,Mouse,C57BL/6,14.5 days,Fetal/E14.5,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Calvaria,Mouse,C57BL/6,1 day,Neonatal,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Heart,Mouse,C57BL/6,1 day,Neonatal,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Muscle,Mouse,C57BL/6,1 day,Neonatal,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Pancreas,Mouse,C57BL/6,1 day,Neonatal,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Rib,Mouse,C57BL/6,1 day,Neonatal,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
MCA,Skin,Mouse,C57BL/6,1 day,Neonatal,https://pubmed.ncbi.nlm.nih.gov/29474909/,"Han, X. et al. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 172, 1091-1107.e17 (2018)."
SCP2038,Colon,Mouse,"KRAS^LSL-G12D/+,APC^fl/fl, Rosa26^LSL-tdTomato, Trp53^fl/fl,Villin^CreERT2",6-10 weeks,Adult,"https://www.biorxiv.org/content/10.1101/2022.10.02.508492v1.full.pdf, https://www.nature.com/articles/s41587-023-01657-3, https://singlecell.broadinstitute.org/single_cell/study/SCP2038/single-cell-and-spatial-transcriptomics-of-mouse-colon?hiddenTraces=2020-09-14_Puck_200701_20#study-summary","Avraham-Davidi, I. et al. Integrative single cell and spatial transcriptomics of colorectal cancer reveals multicellular functional units that support tumor progression. Preprint at bioRxiv (2022) https://www.biorxiv.org/content/10.1101/2022.10.02.508492v1 (2022)."