Reference transcripts

List of reference transcripts used for each cell type in each tissue analysed in the Tissue Cell Type section. A panel of 3 "virtual reference transcripts" with highly cell type specific expression were selected to represent each of the main constituent cell types within each tissue. Reference transcripts were selected based on existing data, including in-house generated immunohistochemically stained tissue sections and published single cell RNAseq data.

Tissue Cell type Reference gene
Adipose subcutaneous Adipocytes (Subcutaneous) ADIPOQ
Adipose subcutaneous Adipocytes (Subcutaneous) PLIN1
Adipose subcutaneous Adipocytes (Subcutaneous) LIPE
Adipose subcutaneous Adipose progenitor cells FKBP10
Adipose subcutaneous Adipose progenitor cells COL6A1
Adipose subcutaneous Adipose progenitor cells COL6A2
Adipose subcutaneous Endothelial cells ESAM
Adipose subcutaneous Endothelial cells MMRN2
Adipose subcutaneous Endothelial cells CDH5
Adipose subcutaneous Macrophages C1QC
Adipose subcutaneous Macrophages FCER1G
Adipose subcutaneous Macrophages CD68
Adipose subcutaneous Mast cells CPA3
Adipose subcutaneous Mast cells TPSB2
Adipose subcutaneous Mast cells TPSAB1
Adipose subcutaneous Plasma cells IGKC
Adipose subcutaneous Plasma cells JCHAIN
Adipose subcutaneous Plasma cells MZB1
Adipose subcutaneous Smooth muscle cells KCNMB1
Adipose subcutaneous Smooth muscle cells MYH11
Adipose subcutaneous Smooth muscle cells CNN1
Adipose subcutaneous T-cells TRBC2
Adipose subcutaneous T-cells CD6
Adipose subcutaneous T-cells CD3E
Adipose visceral Adipocytes (Visceral) ADIPOQ
Adipose visceral Adipocytes (Visceral) PLIN1
Adipose visceral Adipocytes (Visceral) LIPE
Adipose visceral Adipose progenitor cells FKBP10
Adipose visceral Adipose progenitor cells COL6A1
Adipose visceral Adipose progenitor cells COL6A2
Adipose visceral Endothelial cells ESAM
Adipose visceral Endothelial cells MMRN2
Adipose visceral Endothelial cells CDH5
Adipose visceral Macrophages C1QC
Adipose visceral Macrophages FCER1G
Adipose visceral Macrophages CD68
Adipose visceral Mast cells CPA3
Adipose visceral Mast cells TPSB2
Adipose visceral Mast cells TPSAB1
Adipose visceral Mesothelial cells UPK3B
Adipose visceral Mesothelial cells MSLN
Adipose visceral Mesothelial cells KRT19
Adipose visceral Neutrophils CSF3R
Adipose visceral Neutrophils FCGR3B
Adipose visceral Neutrophils CXCR2
Adipose visceral Plasma cells IGKC
Adipose visceral Plasma cells JCHAIN
Adipose visceral Plasma cells MZB1
Adipose visceral Smooth muscle cells KCNMB1
Adipose visceral Smooth muscle cells MYH11
Adipose visceral Smooth muscle cells CNN1
Adipose visceral T-cells TRBC2
Adipose visceral T-cells CD6
Adipose visceral T-cells CD3E
Breast Adipocytes (Breast) ADIPOQ
Breast Adipocytes (Breast) PLIN1
Breast Adipocytes (Breast) LIPE
Breast Breast glandular cells (progenitors) ATP6V0A4
Breast Breast glandular cells (progenitors) TMEM213
Breast Breast glandular cells (progenitors) AQP5
Breast Breast glandular cells_1 MUC1
Breast Breast glandular cells_1 AZGP1
Breast Breast glandular cells_1 PRR15L
Breast Breast glandular cells_2 MYB
Breast Breast glandular cells_2 PRR15
Breast Breast glandular cells_2 PLPPR3
Breast Breast myoepithelial cells EPHB1
Breast Breast myoepithelial cells DKK3
Breast Breast myoepithelial cells FHOD3
Breast Endothelial cells ESAM
Breast Endothelial cells MMRN2
Breast Endothelial cells ERG
Breast Fibroblasts OLFML3
Breast Fibroblasts DCN
Breast Fibroblasts FBLN1
Breast Macrophages C1QC
Breast Macrophages FCER1G
Breast Macrophages CCR1
Breast Plasma cells IGKC
Breast Plasma cells MZB1
Breast Plasma cells IGLC1
Breast Smooth muscle cells FLNA
Breast Smooth muscle cells RASL12
Breast Smooth muscle cells MYH11
Breast T-cells TRBC2
Breast T-cells CD6
Breast T-cells CCL5
Colon Colon enterocytes EPCAM
Colon Colon enterocytes SLC44A4
Colon Colon enterocytes PHGR1
Colon Colon enteroendocrine cells INA
Colon Colon enteroendocrine cells RTN1
Colon Colon enteroendocrine cells SCG3
Colon Endothelial cells ESAM
Colon Endothelial cells MMRN2
Colon Endothelial cells CDH5
Colon Enteric glia cells NRXN1
Colon Enteric glia cells SLC35F1
Colon Enteric glia cells L1CAM
Colon Fibroblasts TNXB
Colon Fibroblasts DCN
Colon Fibroblasts FBLN1
Colon Macrophages C1QB
Colon Macrophages CD68
Colon Macrophages ITGB2
Colon Mast cells CPA3
Colon Mast cells TPSAB1
Colon Mast cells SIGLEC6
Colon Mitotic cells (Colon) RRM2
Colon Mitotic cells (Colon) HMMR
Colon Mitotic cells (Colon) TOP2A
Colon Neutrophils S100A8
Colon Neutrophils AQP9
Colon Neutrophils FCAR
Colon Plasma cells IGKC
Colon Plasma cells JCHAIN
Colon Plasma cells IGHA1
Colon Smooth muscle cells ACTG2
Colon Smooth muscle cells TAGLN
Colon Smooth muscle cells TPM1
Colon T-cells CD2
Colon T-cells CD6
Colon T-cells CD3E
Heart muscle Cardiomyocytes TNNT2
Heart muscle Cardiomyocytes MYBPC3
Heart muscle Cardiomyocytes ACTC1
Heart muscle Endothelial cells ADGRL4
Heart muscle Endothelial cells CD93
Heart muscle Endothelial cells ERG
Heart muscle Fibroblasts MMP2
Heart muscle Fibroblasts FBLN1
Heart muscle Fibroblasts COL6A2
Heart muscle Macrophages C1QC
Heart muscle Macrophages CCR1
Heart muscle Macrophages LYVE1
Heart muscle Mitotic cells (Heart) KIFC1
Heart muscle Mitotic cells (Heart) MKI67
Heart muscle Mitotic cells (Heart) TOP2A
Heart muscle Neutrophils CSF3R
Heart muscle Neutrophils AQP9
Heart muscle Neutrophils MMP25
Heart muscle Plasma cells IGKC
Heart muscle Plasma cells JCHAIN
Heart muscle Plasma cells IGHG1
Heart muscle Smooth muscle cells MYLK
Heart muscle Smooth muscle cells KCNMB1
Heart muscle Smooth muscle cells MYH11
Heart muscle T-cells ITGAL
Heart muscle T-cells CCL5
Heart muscle T-cells TRBC1
Kidney Ascending Loop of Henle cells CLDN19
Kidney Ascending Loop of Henle cells NRK
Kidney Ascending Loop of Henle cells SLC12A1
Kidney Endothelial cells ADGRL4
Kidney Endothelial cells ERG
Kidney Endothelial cells ECSCR
Kidney Fibroblasts DKK3
Kidney Fibroblasts DCN
Kidney Fibroblasts FBLN5
Kidney Intercalated cells ATP6V1G3
Kidney Intercalated cells SLC4A9
Kidney Intercalated cells HEPACAM2
Kidney Macrophages C1QA
Kidney Macrophages VSIG4
Kidney Macrophages CD163
Kidney Plasma cells IGKC
Kidney Plasma cells JCHAIN
Kidney Plasma cells IGHG1
Kidney Podocytes NPHS2
Kidney Podocytes PTPRO
Kidney Podocytes NPHS1
Kidney Proximal tubular cells_1 LRP2
Kidney Proximal tubular cells_1 ACE2
Kidney Proximal tubular cells_1 ANPEP
Kidney Proximal tubular cells_2 AGMAT
Kidney Proximal tubular cells_2 MSRA
Kidney Proximal tubular cells_2 ASPDH
Kidney T-cells CD96
Kidney T-cells TRBC2
Kidney T-cells CD6
Liver Cholangiocyte EPCAM
Liver Cholangiocyte KRT7
Liver Cholangiocyte SPINT1
Liver Erythroid cells CA1
Liver Erythroid cells AHSP
Liver Erythroid cells SLC4A1
Liver Hepatic stellate cells OLFML3
Liver Hepatic stellate cells DCN
Liver Hepatic stellate cells ISLR
Liver Hepatocyte_1 ADH6
Liver Hepatocyte_1 CMBL
Liver Hepatocyte_1 SLC10A1
Liver Hepatocyte_2 C8A
Liver Hepatocyte_2 AOX1
Liver Hepatocyte_2 APOF
Liver Kupffer cells LST1
Liver Kupffer cells IGSF6
Liver Kupffer cells SIGLEC1
Liver Neutrophils CSF3R
Liver Neutrophils S100A8
Liver Neutrophils FPR1
Liver NK-cells (Liver) SH2D1B
Liver NK-cells (Liver) KLRF1
Liver NK-cells (Liver) NCR1
Liver Plasma cells IGKC
Liver Plasma cells JCHAIN
Liver Plasma cells IGLC1
Liver Sinusoid Endothelial cells EHD3
Liver Sinusoid Endothelial cells CLEC1B
Liver Sinusoid Endothelial cells GPR182
Liver T-cells CD6
Liver T-cells CD3E
Liver T-cells CD3D
Liver Vascular Endothelial cells ARAP3
Liver Vascular Endothelial cells RHOJ
Liver Vascular Endothelial cells ECSCR
Lung Alveolar cells type 1 AGER
Lung Alveolar cells type 1 CLIC5
Lung Alveolar cells type 1 EMP2
Lung Alveolar cells type 2 SLC26A9
Lung Alveolar cells type 2 ACOXL
Lung Alveolar cells type 2 CFTR
Lung B-cells MS4A1
Lung B-cells CD19
Lung B-cells TNFRSF13C
Lung Endothelial cells ESAM
Lung Endothelial cells FLI1
Lung Endothelial cells ERG
Lung Fibroblast_1 CAMK2N1
Lung Fibroblast_1 TCF21
Lung Fibroblast_1 GPC3
Lung Fibroblast_2 PODN
Lung Fibroblast_2 FBLN2
Lung Fibroblast_2 SERPINF1
Lung Macrophages C1QA
Lung Macrophages CTSD
Lung Macrophages MS4A4A
Lung Mast cells RGS13
Lung Mast cells CPA3
Lung Mast cells SLC18A2
Lung Mitotic cells (Lung) ANLN
Lung Mitotic cells (Lung) TOP2A
Lung Mitotic cells (Lung) TPX2
Lung Neutrophil_1 MPO
Lung Neutrophil_1 PRTN3
Lung Neutrophil_1 ELANE
Lung Neutrophil_2 GLT1D1
Lung Neutrophil_2 AQP9
Lung Neutrophil_2 FPR1
Lung NK-cells (Lung) SH2D1B
Lung NK-cells (Lung) KLRF1
Lung NK-cells (Lung) NCR1
Lung Plasma cells IGKC
Lung Plasma cells JCHAIN
Lung Plasma cells MZB1
Lung Respiratory ciliated cells ERICH3
Lung Respiratory ciliated cells DNAH12
Lung Respiratory ciliated cells SNTN
Lung Smooth muscle cells TPM2
Lung Smooth muscle cells TAGLN
Lung Smooth muscle cells MYL9
Lung T-cells CD2
Lung T-cells CD3D
Lung T-cells CD3G
Pancreas Alpha cells FEV
Pancreas Alpha cells IRX2
Pancreas Alpha cells ARX
Pancreas Beta cells C1orf127
Pancreas Beta cells G6PC2
Pancreas Beta cells INS
Pancreas Ductal cells_1 CLDN1
Pancreas Ductal cells_1 ANXA3
Pancreas Ductal cells_1 KRT80
Pancreas Ductal cells_2 CRISP3
Pancreas Ductal cells_2 MUC5B
Pancreas Ductal cells_2 ERN2
Pancreas Endothelial cells DIPK2B
Pancreas Endothelial cells MMRN2
Pancreas Endothelial cells ERG
Pancreas Exocrine glandular cells AMY2B
Pancreas Exocrine glandular cells PRSS1
Pancreas Exocrine glandular cells PNLIP
Pancreas Fibroblasts PODN
Pancreas Fibroblasts DCN
Pancreas Fibroblasts FBLN1
Pancreas Macrophages C1QA
Pancreas Macrophages C1QC
Pancreas Macrophages MS4A4A
Pancreas Plasma cells IGKC
Pancreas Plasma cells JCHAIN
Pancreas Plasma cells IGLC2
Pancreas T-cells CD2
Pancreas T-cells CD3E
Pancreas T-cells TRAC
Prostate Endothelial cells ESAM
Prostate Endothelial cells MMRN2
Prostate Endothelial cells CDH5
Prostate Fibroblasts COL14A1
Prostate Fibroblasts DCN
Prostate Fibroblasts FBLN1
Prostate Macrophages C1QA
Prostate Macrophages VSIG4
Prostate Macrophages LRRC25
Prostate Plasma cells IGKC
Prostate Plasma cells JCHAIN
Prostate Plasma cells IGHG1
Prostate Prostate basal glandular cells DLK2
Prostate Prostate basal glandular cells KRT5
Prostate Prostate basal glandular cells FLRT3
Prostate Prostate glandular cells CPNE4
Prostate Prostate glandular cells ACP3
Prostate Prostate glandular cells KLK3
Prostate Smooth muscle cells DES
Prostate Smooth muscle cells MYL9
Prostate Smooth muscle cells JPH2
Prostate T-cells CD2
Prostate T-cells CD6
Prostate T-cells CD3D
Prostate Urothelial cells MUC4
Prostate Urothelial cells TMPRSS4
Prostate Urothelial cells OLFM4
Skeletal muscle Endothelial cells ADGRL4
Skeletal muscle Endothelial cells PECAM1
Skeletal muscle Endothelial cells ERG
Skeletal muscle Fibroblasts LUM
Skeletal muscle Fibroblasts ISLR
Skeletal muscle Fibroblasts SSC5D
Skeletal muscle Macrophages C1QA
Skeletal muscle Macrophages C1QB
Skeletal muscle Macrophages MS4A4A
Skeletal muscle Neutrophils CSF3R
Skeletal muscle Neutrophils VNN2
Skeletal muscle Neutrophils AQP9
Skeletal muscle Plasma cells IGKC
Skeletal muscle Plasma cells JCHAIN
Skeletal muscle Plasma cells IGLC1
Skeletal muscle Skeletal myocytes_1 TNNC1
Skeletal muscle Skeletal myocytes_1 MYL2
Skeletal muscle Skeletal myocytes_1 MYH7
Skeletal muscle Skeletal myocytes_2 MYOZ3
Skeletal muscle Skeletal myocytes_2 APOBEC2
Skeletal muscle Skeletal myocytes_2 PKIA
Skeletal muscle Skeletal myocytes_3 TNNI2
Skeletal muscle Skeletal myocytes_3 TNNT3
Skeletal muscle Skeletal myocytes_3 TPM1
Skeletal muscle Smooth muscle cells ACTG2
Skeletal muscle Smooth muscle cells KCNMB1
Skeletal muscle Smooth muscle cells MYH11
Skin Adipocytes (Skin) PLIN1
Skin Adipocytes (Skin) LIPE
Skin Adipocytes (Skin) TRARG1
Skin Eccrine sweat gland cells CHRM3
Skin Eccrine sweat gland cells SLC12A2
Skin Eccrine sweat gland cells AQP5
Skin Endothelial cells ADGRL4
Skin Endothelial cells MECOM
Skin Endothelial cells DIPK2B
Skin Fibroblast_1 COL3A1
Skin Fibroblast_1 CCDC80
Skin Fibroblast_1 COL1A1
Skin Fibroblast_2 PODN
Skin Fibroblast_2 OLFML3
Skin Fibroblast_2 FBLN2
Skin Hair cortex cells KRTAP2-1
Skin Hair cortex cells KRTAP2-2
Skin Hair cortex cells KRTAP2-4
Skin Inner root sheath cells TCHH
Skin Inner root sheath cells KRT71
Skin Inner root sheath cells KRT25
Skin Keratinocyte (granular) LCE2D
Skin Keratinocyte (granular) LCE1C
Skin Keratinocyte (granular) LCE1B
Skin Keratinocyte (other) DEGS1
Skin Keratinocyte (other) KRT1
Skin Keratinocyte (other) KRT10
Skin Langerhans cells FCER1A
Skin Langerhans cells CSF1R
Skin Langerhans cells LST1
Skin Macrophages C1QB
Skin Macrophages VSIG4
Skin Macrophages CD163
Skin Mast cells RGS13
Skin Mast cells GCSAML
Skin Mast cells MS4A2
Skin Melanocytes MLANA
Skin Melanocytes TYRP1
Skin Melanocytes TYR
Skin Mitotic cells (Skin) CENPF
Skin Mitotic cells (Skin) KIFC1
Skin Mitotic cells (Skin) TOP2A
Skin Outer root sheath cells SLC4A3
Skin Outer root sheath cells LHX2
Skin Outer root sheath cells DACH1
Skin Plasma cells IGKC
Skin Plasma cells JCHAIN
Skin Plasma cells IGLC1
Skin Sebaceous gland cells FADS2
Skin Sebaceous gland cells FADS1
Skin Sebaceous gland cells FAR2
Skin Smooth muscle cells ACTG2
Skin Smooth muscle cells MYH11
Skin Smooth muscle cells CNN1
Skin T-cells CD2
Skin T-cells CD96
Skin T-cells CD3E
Stomach Chief cells PGC
Stomach Chief cells AZGP1
Stomach Chief cells LIPF
Stomach Endothelial cells CDH5
Stomach Endothelial cells PECAM1
Stomach Endothelial cells ERG
Stomach Fibroblasts PCOLCE
Stomach Fibroblasts MMP2
Stomach Fibroblasts CLEC11A
Stomach Gastric enteroendocrine cells ARX
Stomach Gastric enteroendocrine cells ST18
Stomach Gastric enteroendocrine cells INSM1
Stomach Gastric mucous cells CAPN8
Stomach Gastric mucous cells VILL
Stomach Gastric mucous cells LGALS4
Stomach Macrophages C1QB
Stomach Macrophages FCGR3A
Stomach Macrophages ITGB2
Stomach Mitotic cells (Stomach) NCAPH
Stomach Mitotic cells (Stomach) NCAPG
Stomach Mitotic cells (Stomach) KIFC1
Stomach Neutrophils FCGR3B
Stomach Neutrophils CXCR2
Stomach Neutrophils CXCR1
Stomach Parietal cells ATP4B
Stomach Parietal cells ATP4A
Stomach Parietal cells MFSD4A
Stomach Plasma cells IGKC
Stomach Plasma cells JCHAIN
Stomach Plasma cells IGLC1
Stomach T-cells CD2
Stomach T-cells CD3E
Stomach T-cells CD3G
Testis Early spermatids KPNA5
Testis Early spermatids PBK
Testis Early spermatids CEP55
Testis Endothelial cells DIPK2B
Testis Endothelial cells ESAM
Testis Endothelial cells MMRN2
Testis Late spermatids TNP1
Testis Late spermatids PRM2
Testis Late spermatids PRM1
Testis Leydig cells GSTA1
Testis Leydig cells STAR
Testis Leydig cells CYB5A
Testis Macrophages AIF1
Testis Macrophages FOLR2
Testis Macrophages TYROBP
Testis Peritubular cells WNT2B
Testis Peritubular cells PDE5A
Testis Peritubular cells NRIP2
Testis Sertoli cells SUSD3
Testis Sertoli cells SLC52A3
Testis Sertoli cells MARK4
Testis Spermatocytes RBM44
Testis Spermatocytes ANKRD31
Testis Spermatocytes TOP2A
Testis Spermatogonia KDM1B
Testis Spermatogonia MAGEB2
Testis Spermatogonia PIWIL4
Thyroid Endothelial cells MMRN2
Thyroid Endothelial cells CDH5
Thyroid Endothelial cells ERG
Thyroid Fibroblasts SLIT2
Thyroid Fibroblasts ECM2
Thyroid Fibroblasts OLFML1
Thyroid Macrophages C1QC
Thyroid Macrophages C1QB
Thyroid Macrophages MS4A4A
Thyroid Mitotic cells (Thyroid) CENPF
Thyroid Mitotic cells (Thyroid) MKI67
Thyroid Mitotic cells (Thyroid) TOP2A
Thyroid Neutrophils S100A8
Thyroid Neutrophils AQP9
Thyroid Neutrophils FCAR
Thyroid Parafollicular cells CELF3
Thyroid Parafollicular cells GRP
Thyroid Parafollicular cells CHGB
Thyroid Plasma cells IGKC
Thyroid Plasma cells JCHAIN
Thyroid Plasma cells IGHG1
Thyroid Smooth muscle cells KCNMB1
Thyroid Smooth muscle cells ACTA2
Thyroid Smooth muscle cells MYH11
Thyroid T-cells TRBC2
Thyroid T-cells ITGAL
Thyroid T-cells CCL5
Thyroid Thyroid glandular cells_1 TACC2
Thyroid Thyroid glandular cells_1 KNSTRN
Thyroid Thyroid glandular cells_1 IVD
Thyroid Thyroid glandular cells_2 SLC4A4
Thyroid Thyroid glandular cells_2 REEP5
Thyroid Thyroid glandular cells_2 CDH1