I. Immune cell type annotations

R files for 41 datasets of cancer and 11 files for 9 normal tissues with immune cell type annotation by ensemble method

Cancer / Normal Dataset Title Download
BCCGSE123813Clonal replacement of tumor-specific T cells following PD-1 blockade [single cells]
BCCGSE181907Integrated multi-omics reveals the cellular and molecular interactions governing the invasive niche in skin cancer
BRCAGSE110686Single-cell RNA-seq of six thousand purified CD3+ T cells from human primary TNBCs
BRCAGSE114727Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment
BRCAGSE161529scRNA-seq profiling of breast cancer tumors, BRCA1 mutant pre-neoplastic mammary gland cells and normal mammary gland cells
BRCAGSE169657Longer read lengths are required for RNA velocity analysis of single-cell RNA-sequencing with paired immune repertoire and transcriptome profiling
BRCAGSE180878A human breast transcriptome atlas
CHOLGSE125449Tumor cell biodiversity drives microenvironmental reprogramming in liver cancer
CHOLGSE151530Understanding tumor evolution and its clonality by single-cell transcriptomic analysis in liver cancer
CHOLGSE171899High-dimensional single cell analysis of T cells infiltrating human intrahepatic cholangiocarcinoma [scRNA-Seq]
CRCGSE108989Lineage tracking reveals dynamic relationships of T cells in colorectal cancer
CRCGSE136394Single-cell transcriptome analysis reveals gene signatures associated with T-cell persistence following adoptive cell therapy
CRCGSE139555Peripheral clonal expansion of T lymphocytes associates with tumour infiltration and response to cancer immunotherapy
CRCGSE146771Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted therapies in colon cancer
CTCLGSE128531Single-cell lymphocyte heterogeneity inadvanced Cutaneous T-Cell Lymphoma skin tumors
CTCLGSE182861Single-cell RNA sequencing unveils the clonal and transcriptional landscape of cutaneous T-cell lymphomas
GCGSE163558Transcriptional heterogeneity in primary and metastatic gastric cancer revealed using single-cell RNA sequencing
GCGSE183904Single-cell atlas of lineage states, tumor microenvironment and subtype specific expression programs in gastric cancer
HGSOCGSE184880Single-cell RNA sequencing reveals tissue architecture during human high-grade serous ovarian cancer progression
HNSCGSE139324Immune landscape of viral- and carcinogen-drived head and neck cancer
HNSCGSE195832Immunostimulatory cancer-associated fibroblast subpopulations can predict immunotherapy response in head and neck cancer
KIRCGSE111360Organoid modeling of the tumor immune microenvironment
KIRCGSE139555Peripheral clonal expansion of T lymphocytes associates with tumour infiltration and response to cancer immunotherapy
KIRCGSE145281High gene expression of IL8 in peripheral blood mononuclear cells from bladder cancer patients is associated with nonresponders to atezolizumab
LIHCGSE125449Tumor cell biodiversity drives microenvironmental reprogramming in liver cancer
LIHCGSE140228Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma
LIHCGSE98638Landscape of infiltrating T cells in liver cancer revealed by single-cell sequencing
MESOGSE201925Gene expression profile at single cell level of a mesothelioma patient specimen treated with ADU-S100
NSCLCGSE127465Single cell transcriptomics of human and mouse lung cancers reveals conserved myeloid populations across individuals and species
NSCLCGSE131907Single cell RNA sequencing of lung adenocarcinoma
NSCLCGSE139555Peripheral clonal expansion of T lymphocytes associates with tumour infiltration and response to cancer immunotherapy
NSCLCGSE99254T cell landscape of non-small cell lung cancer revealed by deep single-cell RNA sequencing
PAADCRA001160NA
PCaGSE137829Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer
PCaGSE153892Immunoprofiling of prostate cancer infiltrate
PTCGSE184362Single-cell sequencing of tumor ecosystems in papillary thyroid carcinoma
PTCGSE191288Dissecting the transcriptomic landscape of the human papillary thyroid carcinoma by single cell RNA-sequencing
SKCMGSE115978Single-cell RNA-seq of melanoma ecosystems reveals sources of T cells exclusion linked to immunotherapy clinical outcomes
SKCMGSE123139Dysfunctional CD8+ T cells form a proliferative, dynamically regulated compartment within human melanoma [scRNA-seq]
SKCMGSE148190Single cell RNA and TCR sequencing of tumor-infiltrating lymphocytes from human melanoma
UVMGSE137829Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer
BMAConde et al.Cross-tissue immune cell analysis revealstissue-specific features in humans
BMAHCL Bone Marrow1Human Cell Landscape
BMAHCL Bone Marrow2Human Cell Landscape
BMAHCL Bone Marrow3Human Cell Landscape
BMAHCL Bone Marrow4Human Cell Landscape
JEJEPIConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
JEJLPConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
LIVConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
LIVHCL Liver1Human Cell Landscape
LIVHCL Liver2Human Cell Landscape
LIVHCL Liver4Human Cell Landscape
LLNConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
LNGConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
LNGHCL Lung1Human Cell Landscape
LNGHCL Lung2Human Cell Landscape
LNGHCL Lung3Human Cell Landscape
MLNConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
SPLConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
SPLHCL Spleen1Human Cell Landscape
PBMC8k PBMCs from a Healthy Donor8k PBMCs from a Healthy Donor
PBMC33k PBMCs from a Healthy Donor33k PBMCs from a Healthy Donor
PBMC5k_pbmc_NGSC3_aggr5k_pbmc_NGSC3_aggr

II. Marker gene atlas

Top 100 highly expressing genes of each cell type in all scRNA-seq projects annotated by ensemble method

Cancer / Normal Dataset Title Download
CRCGSE146771Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted therapies in colon cancer
CRCGSE139555Peripheral clonal expansion of T lymphocytes associates with tumour infiltration and response to cancer immunotherapy
CHOLGSE125449Tumor cell biodiversity drives microenvironmental reprogramming in liver cancer
GCGSE163558Transcriptional heterogeneity in primary and metastatic gastric cancer revealed using single-cell RNA sequencing
HGSOCGSE184880Single-cell RNA sequencing reveals tissue architecture during human high-grade serous ovarian cancer progression
KIRCGSE139555Peripheral clonal expansion of T lymphocytes associates with tumour infiltration and response to cancer immunotherapy
KIRCGSE145281High gene expression of IL8 in peripheral blood mononuclear cells from bladder cancer patients is associated with nonresponders to atezolizumab
LIHCGSE125449Tumor cell biodiversity drives microenvironmental reprogramming in liver cancer
UVMGSE139829Single-cell analysis reveals new evolutionary complexity in uveal melanoma
BCCGSE181907Integrated multi-omics reveals the cellular and molecular interactions governing the invasive niche in skin cancer
BRCAGSE110686Single-cell RNA-seq of six thousand purified CD3+ T cells from human primary TNBCs
CHOLGSE151530Understanding tumor evolution and its clonality by single-cell transcriptomic analysis in liver cancer
CHOLGSE171899High-dimensional single cell analysis of T cells infiltrating human intrahepatic cholangiocarcinoma [scRNA-Seq]
CTCLGSE128531Single-cell lymphocyte heterogeneity inadvanced Cutaneous T-Cell Lymphoma skin tumors
HNSCGSE195832Immunostimulatory cancer-associated fibroblast subpopulations can predict immunotherapy response in head and neck cancer
KIRCGSE111360Organoid modeling of the tumor immune microenvironment
NSCLCGSE127465Single cell transcriptomics of human and mouse lung cancers reveals conserved myeloid populations across individuals and species
PTCGSE184362Single-cell sequencing of tumor ecosystems in papillary thyroid carcinoma
PAADCRA001160-
BCCGSE123813Clonal replacement of tumor-specific T cells following PD-1 blockade [single cells]
MESOGSE201925Gene expression profile at single cell level of a mesothelioma patient specimen treated with ADU-S100
NSCLCGSE139555Peripheral clonal expansion of T lymphocytes associates with tumour infiltration and response to cancer immunotherapy
BRCAGSE169657Longer read lengths are required for RNA velocity analysis of single-cell RNA-sequencing with paired immune repertoire and transcriptome profiling
HNSCGSE139324Immune landscape of viral- and carcinogen-drived head and neck cancer
PCaGSE153892Immunoprofiling of prostate cancer infiltrate
SKCMGSE115978Single-cell RNA-seq of melanoma ecosystems reveals sources of T cells exclusion linked to immunotherapy clinical outcomes
SKCMGSE123139Dysfunctional CD8+ T cells form a proliferative, dynamically regulated compartment within human melanoma [scRNA-seq]
SKCMGSE148190Single cell RNA and TCR sequencing of tumor-infiltrating lymphocytes from human melanoma
LIHCGSE140228Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma
BRCAGSE114727Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment
BRCAGSE180878A human breast transcriptome atlas
CRCGSE108989Lineage tracking reveals dynamic relationships of T cells in colorectal cancer
CRCGSE136394Single-cell transcriptome analysis reveals gene signatures associated with T-cell persistence following adoptive cell therapy
CTCLGSE182861Single-cell RNA sequencing unveils the clonal and transcriptional landscape of cutaneous T-cell lymphomas
GCGSE183904Single-cell atlas of lineage states, tumor microenvironment and subtype specific expression programs in gastric cancer
LIHCGSE98638Landscape of infiltrating T cells in liver cancer revealed by single-cell sequencing
JEJEPIConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
JEJLPConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
LIVConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
LIVHCL Liver1Human Cell Landscape
LIVHCL Liver2Human Cell Landscape
LIVHCL Liver4Human Cell Landscape
LNGConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
LNGHCL Lung1Human Cell Landscape
LNGHCL Lung2Human Cell Landscape
LNGHCL Lung3Human Cell Landscape
MLNConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
SPLConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
SPLHCL Spleen1Human Cell Landscape
NSCLCGSE99254T cell landscape of non-small cell lung cancer revealed by deep single-cell RNA sequencing
PBMC33k PBMCs from a Healthy Donor33k PBMCs from a Healthy Donor
PBMC5k_pbmc_NGSC3_aggr5k_pbmc_NGSC3_aggr
PBMC8k PBMCs from a Healthy Donor8k PBMCs from a Healthy Donor
PCaGSE137829Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer
PTCGSE191288Dissecting the transcriptomic landscape of the human papillary thyroid carcinoma by single cell RNA-sequencing
BRCAGSE161529scRNA-seq profiling of breast cancer tumors, BRCA1 mutant pre-neoplastic mammary gland cells and normal mammary gland cells
NSCLCGSE131907Single cell RNA sequencing of lung adenocarcinoma
BMAConde et al.Cross-tissue immune cell analysis revealstissue-specific features in humans
BMAHCL Bone Marrow1Human Cell Landscape
BMAHCL Bone Marrow2Human Cell Landscape
BMAHCL Bone Marrow3Human Cell Landscape
BMAHCL Bone Marrow4Human Cell Landscape
LLNConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans

III. scRNA-seq expression profiles

scRNA-seq expression profiles for each project in a compressed format

Cancer / Normal Dataset Title Download
BCCGSE123813Clonal replacement of tumor-specific T cells following PD-1 blockade [single cells]
BCCGSE181907Integrated multi-omics reveals the cellular and molecular interactions governing the invasive niche in skin cancer
BRCAGSE110686Single-cell RNA-seq of six thousand purified CD3+ T cells from human primary TNBCs
BRCAGSE114727Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment
BRCAGSE161529scRNA-seq profiling of breast cancer tumors, BRCA1 mutant pre-neoplastic mammary gland cells and normal mammary gland cells
BRCAGSE169657Longer read lengths are required for RNA velocity analysis of single-cell RNA-sequencing with paired immune repertoire and transcriptome profiling
BRCAGSE180878A human breast transcriptome atlas
CHOLGSE125449Tumor cell biodiversity drives microenvironmental reprogramming in liver cancer
CHOLGSE151530Understanding tumor evolution and its clonality by single-cell transcriptomic analysis in liver cancer
CHOLGSE171899High-dimensional single cell analysis of T cells infiltrating human intrahepatic cholangiocarcinoma [scRNA-Seq]
CRCGSE108989Lineage tracking reveals dynamic relationships of T cells in colorectal cancer
CRCGSE136394Single-cell transcriptome analysis reveals gene signatures associated with T-cell persistence following adoptive cell therapy
CRCGSE139555Peripheral clonal expansion of T lymphocytes associates with tumour infiltration and response to cancer immunotherapy
CRCGSE146771Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted therapies in colon cancer
CTCLGSE128531Single-cell lymphocyte heterogeneity inadvanced Cutaneous T-Cell Lymphoma skin tumors
CTCLGSE182861Single-cell RNA sequencing unveils the clonal and transcriptional landscape of cutaneous T-cell lymphomas
GCGSE163558Transcriptional heterogeneity in primary and metastatic gastric cancer revealed using single-cell RNA sequencing
GCGSE183904Single-cell atlas of lineage states, tumor microenvironment and subtype specific expression programs in gastric cancer
HGSOCGSE184880Single-cell RNA sequencing reveals tissue architecture during human high-grade serous ovarian cancer progression
HNSCGSE139324Immune landscape of viral- and carcinogen-drived head and neck cancer
HNSCGSE195832Immunostimulatory cancer-associated fibroblast subpopulations can predict immunotherapy response in head and neck cancer
KIRCGSE111360Organoid modeling of the tumor immune microenvironment
KIRCGSE139555Peripheral clonal expansion of T lymphocytes associates with tumour infiltration and response to cancer immunotherapy
KIRCGSE145281High gene expression of IL8 in peripheral blood mononuclear cells from bladder cancer patients is associated with nonresponders to atezolizumab
LIHCGSE125449Tumor cell biodiversity drives microenvironmental reprogramming in liver cancer
LIHCGSE140228Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma
LIHCGSE98638Landscape of infiltrating T cells in liver cancer revealed by single-cell sequencing
MESOGSE201925Gene expression profile at single cell level of a mesothelioma patient specimen treated with ADU-S100
NSCLCGSE127465Single cell transcriptomics of human and mouse lung cancers reveals conserved myeloid populations across individuals and species
NSCLCGSE131907Single cell RNA sequencing of lung adenocarcinoma
NSCLCGSE139555Peripheral clonal expansion of T lymphocytes associates with tumour infiltration and response to cancer immunotherapy
NSCLCGSE99254T cell landscape of non-small cell lung cancer revealed by deep single-cell RNA sequencing
PAADCRA001160NA
PCaGSE137829Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer
PCaGSE153892Immunoprofiling of prostate cancer infiltrate
PTCGSE184362Single-cell sequencing of tumor ecosystems in papillary thyroid carcinoma
PTCGSE191288Dissecting the transcriptomic landscape of the human papillary thyroid carcinoma by single cell RNA-sequencing
SKCMGSE115978Single-cell RNA-seq of melanoma ecosystems reveals sources of T cells exclusion linked to immunotherapy clinical outcomes
SKCMGSE123139Dysfunctional CD8+ T cells form a proliferative, dynamically regulated compartment within human melanoma [scRNA-seq]
SKCMGSE148190Single cell RNA and TCR sequencing of tumor-infiltrating lymphocytes from human melanoma
UVMGSE137829Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer
BMAConde et al.Cross-tissue immune cell analysis revealstissue-specific features in humans
BMAHCL Bone Marrow1Human Cell Landscape
BMAHCL Bone Marrow2Human Cell Landscape
BMAHCL Bone Marrow3Human Cell Landscape
BMAHCL Bone Marrow4Human Cell Landscape
JEJEPIConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
JEJLPConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
LIVConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
LIVHCL Liver1Human Cell Landscape
LIVHCL Liver2Human Cell Landscape
LIVHCL Liver4Human Cell Landscape
LLNConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
LNGConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
LNGHCL Lung1Human Cell Landscape
LNGHCL Lung2Human Cell Landscape
LNGHCL Lung3Human Cell Landscape
MLNConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
SPLConde et al.Cross-tissue immune cell analysis reveals tissue-specific features in humans
SPLHCL Spleen1Human Cell Landscape
PBMC8k PBMCs from a Healthy Donor8k PBMCs from a Healthy Donor
PBMC33k PBMCs from a Healthy Donor33k PBMCs from a Healthy Donor
PBMC5k_pbmc_NGSC3_aggr5k_pbmc_NGSC3_aggr