diff --git a/assets/json/mouse_pansci.json b/assets/json/mouse_pansci.json new file mode 100644 index 00000000..694f2669 --- /dev/null +++ b/assets/json/mouse_pansci.json @@ -0,0 +1,106 @@ +{ + "version": "1.0.0", + "name": "Mouse Pansci", + "datasets": [ + { + "uid": "mouse-pansci", + "name": "Mouse Pansci", + "files": [ + { + "type": "cells", + "fileType": "anndata-cells.zarr", + "url": "https://azimuth-vitessce.s3.us-west-2.amazonaws.com/mouse_pansci/vitessce_ref.zarr", + "options": { + "mappings": { + "UMAP": { + "key": "obsm/X_umap", + "dims": [ + 0, + 1 + ] + } + }, + "factors": [ + "obs/Main_cell_type", + "obs/Sub_cell_type", + "obs/Sub_cell_type_organ" + ] + } + }, + { + "type": "cell-sets", + "fileType": "anndata-cell-sets.zarr", + "url": "https://azimuth-vitessce.s3.us-west-2.amazonaws.com/mouse_pansci/vitessce_ref.zarr", + "options": [ + { + "groupName": "Main_cell_type", + "setName": "obs/Main_cell_type" + }, + { + "groupName": "Sub_cell_type", + "setName": "obs/Sub_cell_type" + }, + { + "groupName": "Sub_cell_type_organ", + "setName": "obs/Sub_cell_type_organ" + } + ] + }, + { + "type": "expression-matrix", + "fileType": "anndata-expression-matrix.zarr", + "url": "https://azimuth-vitessce.s3.us-west-2.amazonaws.com/mouse_pansci/vitessce_ref.zarr", + "options": { + "matrix": "X" + } + } + ] + } + ], + "initStrategy": "auto", + "coordinationSpace": { + "embeddingType": { + "UMAP": "UMAP" + }, + "embeddingCellRadius": { + "UMAP": 0.03 + }, + "embeddingCellSetLabelsVisible": { + "UMAP": true + }, + "embeddingCellSetLabelSize": { + "UMAP": 10 + } + }, + "layout": [ + { + "component": "cellSets", + "h": 3, + "w": 3, + "x": 9, + "y": 0, + "coordinationScopes": {} + }, + { + "component": "genes", + "h": 3, + "w": 3, + "x": 9, + "y": 3, + "coordinationScopes": {} + }, + { + "component": "scatterplot", + "h": 6, + "w": 9, + "x": 0, + "y": 0, + "coordinationScopes": { + "embeddingType": "UMAP", + "embeddingCellRadius": "UMAP", + "embeddingCellSetLabelsVisible": "UMAP", + "embeddingCellSetLabelSize": "UMAP" + } + } + ] +} diff --git a/assets/mouse_pansci.jsx b/assets/mouse_pansci.jsx new file mode 100644 index 00000000..152163ce --- /dev/null +++ b/assets/mouse_pansci.jsx @@ -0,0 +1,22 @@ +const React = window.React; +const ReactDOM = window.ReactDOM; +const { Vitessce } = window.vitessce.index; +import myViewConfig from 'json/mouse_pansci.json'; + +function MyVitessce() { + return ( +
+ +
+ ); +} + +function renderMyVitessce() { + ReactDOM.render(, document.getElementById("vitessce")); +} + +renderMyVitessce(); diff --git a/content/_index.md b/content/_index.md index e3b8dbeb..9bf3f654 100644 --- a/content/_index.md +++ b/content/_index.md @@ -8,7 +8,7 @@ type: "static" Azimuth is a web application that uses an annotated reference dataset to automate the processing, analysis, and interpretation of a new single-cell RNA-seq or ATAC-seq experiment. Azimuth leverages a 'reference-based mapping' pipeline that inputs a counts matrix and performs normalization, visualization, cell annotation, and differential expression (biomarker discovery). All results can be explored within the app, and easily downloaded for additional downstream analysis.

-The development of Azimuth is led by the New York Genome Center Mapping Component as part of the [NIH Human Biomolecular Atlas Project (HuBMAP)](https://commonfund.nih.gov/hubmap). Thirteen molecular reference maps are currently available, with more coming soon. +The development of Azimuth is led by the New York Genome Center Mapping Component as part of the [NIH Human Biomolecular Atlas Project (HuBMAP)](https://commonfund.nih.gov/hubmap). Fourteen molecular reference maps are currently available, with more coming soon. {{< /section >}} diff --git a/content/references/mouse_pansci/index.md b/content/references/mouse_pansci/index.md new file mode 100644 index 00000000..913ed1b0 --- /dev/null +++ b/content/references/mouse_pansci/index.md @@ -0,0 +1,11 @@ +--- +type: "static" +---- +{{< section >}} + +# Mouse Pansci Reference Explorer + +{{< /section >}} + +{{< vitessce script="mouse_pansci.jsx" >}} +{{< vitessce_marker_tables ref="Mouse - Pansci" >}} diff --git a/data/azimuth_references.yaml b/data/azimuth_references.yaml index 79ce7464..54db39c1 100644 --- a/data/azimuth_references.yaml +++ b/data/azimuth_references.yaml @@ -327,3 +327,22 @@ file: tonsil_v2_l1.csv - name: celltype.l2 file: tonsil_v2_l2.csv + +- title: Mouse - Pansci + applink: https://app.azimuth.hubmapconsortium.org/app/mouse_pansci + image: mousepansciumap.png + snakemake: https://github.com/satijalab/azimuth-references/tree/master/mouse_pansci + zenodo: TBD + vitessce: /references/mouse_pansci + modalities: RNA + unit: Cells + nunit: 488,526 + species: Mouse + demodata: "[Emont et al., 2022.](https://www.nature.com/articles/s41586-022-04518-2)" + dataref: | + [Zhang et al., 2024](https://www.biorxiv.org/content/10.1101/2024.03.01.583001v1) + details: | + This reference consists of 488,526 cells, with a uniform subsample of 120 cells per subtype from the PanSci mouse organismal aging atlas. Cells were sourced from 14 mouse organs/tissue, including brain, lung, heart, liver, kidney, muscle, stomach, duodenum, jejunum, ileum, colon, brown adipose tissue, inguinal adipose tissue, gonadal adipose tissue, across three different genetic backgrounds: C57BL/6, B6.129S7-Rag1tm1Mom/J, and B6.Cg-Prkdcscid/SzJ. The library for each organ/tissue was constructed using a refined version of the EasySci protocol. Below, we include markers for only the "Main_cell_type" annotation level, which is the most general annotation level in the reference. There are also two more levels of annotation included in the azimuth app. + annotations: + - name: Main_cell_type + file: mouse_pansci_l1.csv diff --git a/static/csv/gut_l1.csv b/static/csv/gut_l1.csv deleted file mode 100644 index 49cd5f22..00000000 --- a/static/csv/gut_l1.csv +++ /dev/null @@ -1,9 +0,0 @@ -"","Label","Markers" -"1","B","MS4A1, CD79A, CD37, CD79B, LTB, CD52, TCL1A, BANK1, VPREB3, POU2F2" -"2","Cholangiocyte","ANXA4, KRT7, DEFB1, FXYD2, TM4SF4, KRT19, KRT8, TACSTD2, EGRI1, SPP1" -"3","Endothelial","FCN3, DNASE1L3, CRHBP, AKAP12, CLEC4G, FCN2, IFI27, IGFBP7, LIFR, ID1" -"4","Hepatocyte","FABP1, CYP2E1, HP, ORM1, APOA2, ADH4, TTR, APOA1, APOC1, APOC3" -"5","HSC/mFB","DCN, ACTA2, IGFBP3, IGFBP7, COLEC11, MYL9, COL1A1, COL3A1, RGS5, TPM2" -"6","Myeloid","C1QB, C1QA, LYZ, S100A9, S100A8, TYROBP, AIF1, LST1, CST3, HLA-DRA" -"7","Plasma","IGLL5, MZB1, DERL3, SSR4, FKBP11, XBP1, SEC11C, ITM2C, HERPUD1, CD27" -"8","T/NK","CCL5, KLRB1, NKG7, GZMA, CCL4, IL7R, CD69, CST7, GZMK, CD3D" diff --git a/static/csv/gut_l2.csv b/static/csv/gut_l2.csv deleted file mode 100644 index 48a8a5b1..00000000 --- a/static/csv/gut_l2.csv +++ /dev/null @@ -1,24 +0,0 @@ -"","Label","Markers" -"1","B","MS4A1, CD79A, CD37, CD79B, LTB, CD52, TCL1A, BANK1, VPREB3, POU2F2" -"2","CD4 T","IL7R, KLRB1, LTB, CD69, CD3D, CD2, CD3E, IL32, SPOCK2, GZMK" -"3","CD8 T","CCL5, CD8A, GZMK, CD3D, CD8B, CD3E, CD2, DUSP2, CD69, CST7" -"4","Cholangiocyte","ANXA4, KRT7, DEFB1, FXYD2, TM4SF4, KRT19, KRT8, TACSTD2, EGRI1, SPP1" -"5","DC1","HLA-DPB1, LGALS2, HLA-DQB1, HLA-DQA1, CLEC9A, CPVL, SNX3, TACSTD2, CST3, CD74" -"6","DC2","HLA-DPB1, HLA-DPA1, HLA-DRA, HLA-DQB1, HLA-DQA1, CLEC10A, FCER1A, LYZ, CD1C, LST1" -"7","Erythrocyte","HBB, HBA1, HBA2, HBD, AHSP, ALAS2, CA1, HBM, SLC25A37, SNCA" -"8","Hepatocyte","FABP1, CYP2E1, HP, ORM1, APOA2, ADH4, TTR, APOA1, APOC1, APOC3" -"9","HSC","IGFBP3, DCN, CXCL14, COLEC11, BGN, CXCL12, ANGPTL6, TMEM56, ECM1, COL3A1" -"10","Inflammatory Macrophage","C1QC, C1QB, C1QA, GPNMB, FABP5, LIPA, CD68, FTL, HLA-DRA, CD9" -"11","Mast","TPSAB1, TPSB2, MALAT1, HPGDS, CTSG, CPA3, VIM, AREG, CD69, CMA1" -"12","Monocyte","S100A8, S100A9, FCN1, LYZ, VCAN, S100A12, LST1, S100A4, MNDA, CSTA" -"13","Myofibroblast","ADIRF, NDUFA4L2, CALD1, C11orf96, NOTCH3, FRZB, MYH11, ACTA2, TPM1, GPX3" -"14","NK","GNLY, NKG7, KLRD1, CMC1, CD7, PRF1, KLRF1, FGFBP2, GZMB, SPON2" -"15","NK_CD56bright","CCL4, CCL3, CD160, KLRB1, NKG7, MALAT1, CMC1, XCL1, CD7, TYROBP" -"16","Noninflammatory Macrophage","MARCO, CD5L, C1QB, C1QA, C1QC, MS4A7, CD163, FTL, CETP, VCAM1" -"17","pDC","GZMB, IRF7, GPR183, LILRA4, PLD4, IRF8, BCL11A, ITM2C, PLAC8, UGCG" -"18","Plasma","IGLL5, MZB1, DERL3, SSR4, FKBP11, XBP1, SEC11C, ITM2C, HERPUD1, CD27" -"19","Portal Fibroblast","THY1, CCL2, PTGDS, ELN, MFAP4, IGFBP7, FBLN1, COL1A2, ACTA2, IGFBP5" -"20","Proliferating T/NK","HIST1H4C, HMGB2, STMN1, MKI67, TUBB, TOP2A, H2AFZ, UBE2C, RRM2, PCNA" -"21","Sinusoidal Endothelial","FCN3, LYVE1, STAB2, FCGR2B, CLEC4G, CRHBP, FLT4, FCN2, CLEC1B, DNASE1L3" -"22","Vascual Central Venous Endothelial","PRSS23, SELE, RSPO3, LXH6, RAMP3, LIFR, LYPD2, NTS, IFI27, DNASE1L3" -"23","Vascual Portal Endothelial","CLEC14A, TM4SF1, ID1, PECAM1, DLL4, MGP, SPARCL1, SLC9A3R2, RAMP2, VWF" diff --git a/static/csv/gut_l3.csv b/static/csv/gut_l3.csv deleted file mode 100644 index 48a8a5b1..00000000 --- a/static/csv/gut_l3.csv +++ /dev/null @@ -1,24 +0,0 @@ -"","Label","Markers" -"1","B","MS4A1, CD79A, CD37, CD79B, LTB, CD52, TCL1A, BANK1, VPREB3, POU2F2" -"2","CD4 T","IL7R, KLRB1, LTB, CD69, CD3D, CD2, CD3E, IL32, SPOCK2, GZMK" -"3","CD8 T","CCL5, CD8A, GZMK, CD3D, CD8B, CD3E, CD2, DUSP2, CD69, CST7" -"4","Cholangiocyte","ANXA4, KRT7, DEFB1, FXYD2, TM4SF4, KRT19, KRT8, TACSTD2, EGRI1, SPP1" -"5","DC1","HLA-DPB1, LGALS2, HLA-DQB1, HLA-DQA1, CLEC9A, CPVL, SNX3, TACSTD2, CST3, CD74" -"6","DC2","HLA-DPB1, HLA-DPA1, HLA-DRA, HLA-DQB1, HLA-DQA1, CLEC10A, FCER1A, LYZ, CD1C, LST1" -"7","Erythrocyte","HBB, HBA1, HBA2, HBD, AHSP, ALAS2, CA1, HBM, SLC25A37, SNCA" -"8","Hepatocyte","FABP1, CYP2E1, HP, ORM1, APOA2, ADH4, TTR, APOA1, APOC1, APOC3" -"9","HSC","IGFBP3, DCN, CXCL14, COLEC11, BGN, CXCL12, ANGPTL6, TMEM56, ECM1, COL3A1" -"10","Inflammatory Macrophage","C1QC, C1QB, C1QA, GPNMB, FABP5, LIPA, CD68, FTL, HLA-DRA, CD9" -"11","Mast","TPSAB1, TPSB2, MALAT1, HPGDS, CTSG, CPA3, VIM, AREG, CD69, CMA1" -"12","Monocyte","S100A8, S100A9, FCN1, LYZ, VCAN, S100A12, LST1, S100A4, MNDA, CSTA" -"13","Myofibroblast","ADIRF, NDUFA4L2, CALD1, C11orf96, NOTCH3, FRZB, MYH11, ACTA2, TPM1, GPX3" -"14","NK","GNLY, NKG7, KLRD1, CMC1, CD7, PRF1, KLRF1, FGFBP2, GZMB, SPON2" -"15","NK_CD56bright","CCL4, CCL3, CD160, KLRB1, NKG7, MALAT1, CMC1, XCL1, CD7, TYROBP" -"16","Noninflammatory Macrophage","MARCO, CD5L, C1QB, C1QA, C1QC, MS4A7, CD163, FTL, CETP, VCAM1" -"17","pDC","GZMB, IRF7, GPR183, LILRA4, PLD4, IRF8, BCL11A, ITM2C, PLAC8, UGCG" -"18","Plasma","IGLL5, MZB1, DERL3, SSR4, FKBP11, XBP1, SEC11C, ITM2C, HERPUD1, CD27" -"19","Portal Fibroblast","THY1, CCL2, PTGDS, ELN, MFAP4, IGFBP7, FBLN1, COL1A2, ACTA2, IGFBP5" -"20","Proliferating T/NK","HIST1H4C, HMGB2, STMN1, MKI67, TUBB, TOP2A, H2AFZ, UBE2C, RRM2, PCNA" -"21","Sinusoidal Endothelial","FCN3, LYVE1, STAB2, FCGR2B, CLEC4G, CRHBP, FLT4, FCN2, CLEC1B, DNASE1L3" -"22","Vascual Central Venous Endothelial","PRSS23, SELE, RSPO3, LXH6, RAMP3, LIFR, LYPD2, NTS, IFI27, DNASE1L3" -"23","Vascual Portal Endothelial","CLEC14A, TM4SF1, ID1, PECAM1, DLL4, MGP, SPARCL1, SLC9A3R2, RAMP2, VWF" diff --git a/static/csv/mouse_pansci_l1.csv b/static/csv/mouse_pansci_l1.csv new file mode 100644 index 00000000..7e61f7f5 --- /dev/null +++ b/static/csv/mouse_pansci_l1.csv @@ -0,0 +1,128 @@ +"","Label","Marker" +"1","Adipoce stem and progenitor cells","Bmper, C7, Fbn1, Col6a5, Gas7, Slit3, Tnfaip6, Adamts12, Ebf2, Vit" +"2","Adipocytes","Ghr, Tenm4, Acaca, Me1, Slc27a1, Fam13a, Acacb, Art3, Nrg4, Gm4876" +"3","Alox15 positive cells","Alox15, Padi4, Tgfb2, Gm13986, Wnt2, Laptm5, Slpi, 4930455G09Rik, Gm4035, Gm29397" +"4","Ascending thin limb of LOH cells","4930407G08Rik, Tbpl2, Nr2e3, Slco4a1, Uncx, 1700016C15Rik, Angpt2, Wnt8b, D630014O11Rik, C330013F16Rik" +"5","Asic2 positive cells","Gm4804, Cpxm2, Sfrp5, Gm15404, Gjb2, Mfap5, Sept6, Fxyd6, Gm6614, Cldn1" +"6","Astrocytes","Slc1a2, Gfap, Slc6a11, Grm3, Arhgef4, Slco1c1, Gm13325, Myoc, Ntsr2, Gm13322" +"7","Atrial cardiomyocytes","Nppa, Bmp10, Fgf12, Pam, Kcnj3, Ankrd1, Gm12381, Dkk3, Epha4, Myl4" +"8","Basal cells","Msln, Ces1h, Tiam1, Ccl20, Ifitm10, Calcoco1, Plekhg1, Fmo6, Tbx1, Ces2f" +"9","Bergmann glia","Luzp2, A2m, Actbl2, Gm5089, Nwd1, Gareml, Gm3764, Gm29521, Msx2, RP23-340C13.4" +"10","Brown adipocytes","Gmpr, Kcnk3, Adra1a, Xrcc6, Col27a1, Dio2, Gm11769, Slc36a2, Gm10032, Ucp1" +"11","Cacna1b positive cells","Ngf, Gstp2, Ccbl1, Mug2, Lcn2, Serpina1b, Gpc3, 2310034O05Rik, Cyp2a5, 1700084C01Rik" +"12","Cerebellum granule neurons","Copg2, Nefm, Nefh, Nefl, Gabra6, Cbln3, Cbln1, Barhl2, Gm12116, Zic2" +"13","Cerebellum interneurons","Skor1, Bhlhe22, Ssxb5, Prdm8, Gm12198, Ccdc27, Trim67, Gm27199, Gm14204, Slc32a1" +"14","Chief cells","Gm12298, D930019O06Rik, Amy2a1, 4930509E16Rik, Mettl21b, CH25-241D1.1, Gm11963, Gm13420, Arntl2, Gm15889" +"15","Cholangiocytes","Tfpi2, E130309D02Rik, Gm830, Bend5, 1810008I18Rik, Slc45a3, Fam198a, 4930486I03Rik, Urah, Setd1a" +"16","Choroid plexus epithelial cells","Enpp2, Htr2c, Trpm3, Ttr, Wdr17, Slc4a10, Gmnc, Otx2os1, Cngb3, Otx2" +"17","Ciliated cells","Scgb1a1, Sec14l3, Cdc20b, Cyp2f2, Lrrc23, Pbx1, Dnah6, Cbr2, Cep128, E030010N08Rik" +"18","Circulating hepatoblasts","Cp, Cyp7b1, Egfr, Pzp, Cps1, Trf, Adk, Pid1, Cfh, Slc7a2" +"19","Colec10 positive cells","Nr1h5, Adamts13, Colec10, Gdf2, Lhx2, Colec11, Rbp1, Gm6277, RP23-331M15.1, Gm16113" +"20","Colonic epithelial cells","Slc26a2, Tgm3, Car4, Saa1, Parm1, Ly6g, Bmp2, Fth1, Slc26a3, Ly6a" +"21","Connecting tubule cells","Tfcp2l1, Klk1, Npnt, Pkhd1, Aqp2, Cdkl1, Aqp3, Veph1, Myh10, Col4a4" +"22","Cortical projection neurons 1","Dcc, Il1rapl1, Npsr1, Ntrk2, E530001K10Rik, Cacna2d3, Gpc5, Gm27247, Lrp1b, Rasgrf1" +"23","Cortical projection neurons 2","Grm4, Thsd7b, Gm15338, Kcnip3, Dpp10, 3110035E14Rik, Sdk2, Olfr114, Sema5b, Srcin1" +"24","Cortical projection neurons 3","Zfp804b, Olfm3, Kctd16, Ntng2, Stk32c, Tmem178, Slc24a2, 1700023F02Rik, Bdnf, 6530402F18Rik" +"25","Dentate gyrus neurons","Rgs7, Sorcs3, Brinp1, Galnt14, Dlgap2, Baiap2, Bai1, Mapk4, Homer1, Lrfn5" +"26","Descending thin limb of LOH cells","Park2, Slc4a11, Fst, Tbpl2, Bdh2, 4930407G08Rik, Lypd2, Trim60, Car14, RP24-393L8.1" +"27","Distal convoluted tubule cells","Slc12a3, Wnk1, Abca13, Defb1, Klhl3, Sfrp1, Clcnkb, Ppp1r1a, Kctd1, Tsc22d1" +"28","Endocardial endothelial cells","Inhba, Rps6ka2, Sncaip, Emcn, Vcam1, Adh6b, Igf2, Rdx, Nos3, Slc26a10" +"29","Endothelial cells","Atp13a5, Gm5127, Fbln5, Zic3, Ltbp4, RP24-287C2.1, Gm12868, Zic2, Nos3, Itm2a" +"30","Enteric glia","Rasgef1c, Gpr37l1, Tmprss5, Gm14267, Gm12688, Kank4, Adam11, Cmtm5, Lgi4, Kcna1" +"31","Enteric neurons","Fam155a, Fgf13, Cntnap2, Asic2, Kcnb2, Pcdh9, Sgcz, Lingo2, Kcnd2, Zfp804a" +"32","Enteroendocrine cells","Chgb, Nts, Gip, Chga, Mctp2, Asic5, Tph1, Pappa2, Rfx6, Gcg" +"33","Ependymal cells","Sspo, Tas2r113, RP24-400J22.2, Gm10714, 4930519F16Rik, RP23-300L15.1, Olfr1512, Vmn2r44, Olfr1511, RP24-461L18.2" +"34","Epididymal cells","Akr1b7, Crisp1, Wdr25, 5430419D17Rik, Pax2, Rgs6, Plcb1, 1700112E06Rik, Fam129a, Ptgs2" +"35","Erythroblasts","Slc25a21, Specc1, Zdhhc14, Sptb, Prim2, Bcl11a, Ank1, Rhag, Hbb-bs, Pvt1" +"36","Fcgbp positive cells","Trps1, Ptn, Stc2, Wnt5b, Cyp3a57, Fbn2, Sema4c, BC006965, Btn1a1, Mlph" +"37","Fibroblasts","Dmbt1, Cyp2c55, Car1, Col6a1, Slc37a2, Col6a2, Col6a4, Htr4, Col6a3, Col4a1" +"38","Fibro–adipogenic progenitors","Prg4, Zfp385b, Scara3, Fndc1, Scara5, Nova1, Abca8a, Smoc2, Medag, Snrpa1" +"39","Fut9 positive cells","Meg3, Tenm2, Lsamp, Fgf14, Ank2, Syt1, Tmem132d, Unc5c, Elavl2, Pde4b" +"40","Gastric epithelial cells","Ank, Cemip, Gm94, Lipm, Aim1, Aadacl3, Aox4, Skint6, Tmprss11f, Pla2g4e" +"41","Gastric mucous cells","Rptn, RP23-227A12.3, Krt78, Gm15318, A4gnt, Prima1, Teddm3, Sfta2, Sox21, Cxcl17" +"42","Goblet cells","Fgfr2, Tmem56, Lct, Abcc2, Jarid2, Cyp3a25, Mme, Dab1, Gm22179, Klhl32" +"43","Habenula neurons","Nwd2, Kcnma1, Kctd8, Cdh10, Gm29478, Robo3, Olfr723, Gabbr2, Gpr139, Lrrc55" +"44","Hepatic stellate cells","Serpina1e, Apoe, Serpina3k, Apoc1, Aox3, Fgb, Mup3, Apoa2, Gc, Hpx" +"45","Hepatocytes","Zfp395, Serpind1, Mup2, Gm20319, Gm29475, 1110008F13Rik, Mvd, Gm3839, Ikbkg, Ftcd" +"46","Hindbrain neurons 1","Lgi2, Vmn2r-ps9, Gm20058, Grm2, Gm14204, Scrg1, Vmn2r5, Gm20657, Gm26939, 1700109G14Rik" +"47","Hindbrain neurons 2","Vwc2l, Cdh23, Zmat4, Adamts2, Gm15645, Bcan, Cpne9, Il1rapl2, Crhr1, Lzts1" +"48","Inferior olivary nucleus neurons","Nrcam, Foxp2, Nell2, 2600014E21Rik, Rims4, Gm5974, Htr5b, Haglr, Gm23326, Gm15393" +"49","Interbrain and midbrain neurons 1","Lrrc7, Gabra4, Adarb1, Abhd12b, Tspear, Lrrn2, Kcnj9, Lhx9, Hrh3, Grin2b" +"50","Interbrain and midbrain neurons 2","Rora, Dok5, Grik2, Tph2, Calcr, Gabra5, Miat, Sorcs1, Fam135b, Zim1" +"51","Interneurons 1","Grip1, Gria1, Galntl6, Cntnap4, Nxph1, Cntnap5c, Pou6f2, Trhde, Lrrc4, Crhbp" +"52","Interneurons 2","Adarb2, Npas3, Dync1i1, Dlx6os1, Cplx2, Cntn4, Sobp, Nkain3, Neto1, 4930555F03Rik" +"53","Interstitial cells of Cajal","Barx1, Spry4, Gm4131, Rem1, Armcx2, RP23-53H1.3, Fibin, Tnn, Gpr173, Dact3" +"54","Intestinal epithelial cells","Pcsk5, Clec2h, 2900026A02Rik, Malrd1, Epcam, Enpep, Myo1d, Mep1b, Cdhr2, Ace2, Krt20, Slc15a1, Ezr, Slc43a2, Xdh, Fabp2, AI747448, Magi1, Abcb1a, Nckap5, Gmds, Cubn, Rrbp1, Reg3b, Sepp1, Plb1, Enpp3, Clca6, Rnf213, Ddx60, mt-Co1, Ext1, Clca3, Atp2b1, Ahnak" +"55","Juxtaglomerular cells","Ren1, Ndst3, Cep112, Nkx3-1, Alx1, 1700066O22Rik, Gm16340, Hey2, Pcdh18, Nrip2" +"56","Lgr5 positive cells","3110099E03Rik, Mannr, Miox, Fam181b, Cyp1a1, Ssu2, Igdcc3, Slco4a1, RP23-212H4.3, Dhh" +"57","Lymphatic endothelial cells","4930435H24Rik, F8, Mmrn1, Neo1, Slc41a1, Flt4, Klhl4, Rnf220, Gm15581, Fam43a" +"58","Lymphoid cells","Ighm, Sox5, Klhl6, Dach2, Gm14005, Ezh2, BE692007, Arid5a, Satb1, Fam169b" +"59","Lymphoid cells_B cells","Cnot6l, Gm15987, Blnk, Dock10, Lipc, Bcl6, Insig2, St3gal1, Rrp1b, St8sia6" +"60","Lymphoid cells_Cycling B cells","Bach2, Parp8, Rhoh, Chrna9, Map4k1, Nuggc, Il21r, Mybl1, Dck, Mef2b" +"61","Lymphoid cells_Plasma cells","Ighg2b, Ighg1, Ighv9-3, Ighg3, Ighj4, Abcc4, Gclc, Dock2, Znrf3, Ighv3-6" +"62","Lymphoid cells_Resting B cells","Nlrc3, Gpr18, H2-Oa, Ccr6, Tnfrsf13c, H2-Eb2, Gm18342, Fcrl1, Cd79a, H2-Ob" +"63","Lymphoid cells_T cells","Themis, 5830411N06Rik, Il2ra, Crtam, Il23r, Lef1, Il7r, Cd5, Icos, Tnfsf8" +"64","Macula densa cells","Slc12a1, Erbb4, Fxyd2, Enox1, Sostdc1, Sec14l1, Casr, Gm16076, Col5a2, Pamr1" +"65","Megf11 positive cells","Greb1l, Akr1b3, Clcnka, Bsnd, Folr1, Gm13075, Cldn19, Sim2, Lypd2, Ugt8a" +"66","Mesothelial cells","Abcb1b, Caln1, Fn1, Adamtsl1, Mast4, Pkhd1l1, Kazn, Gpm6a, Has1, Upk3b" +"67","Mfge8 positive cells","Mfge8, Fcamr, Hpse2, Ccl21a, S1pr3, Dchs2, Edar, Cxcl13, Cr2, Stra6" +"68","Microglia","RP23-247J17.2, Crybb1, RP23-247J17.3, Ifi202b, AY512915, Trem2, Gpr34, Gal3st4, Gm26680, Tmem119" +"69","Mirg positive cells","Phka1, Rian, B830012L14Rik, RP23-204I16.3, Mirg, Gm14261, Asb14, Mir1a-1, Mir341, Pfkfb3" +"70","Muc2-producing goblet cells","Odf2l, Saysd1, Ptgdr, RP24-441N3.3, Pdx1, Gm26801, Gm12506, Grin1os, Rap1gapos, Lrrc26" +"71","Muc5ac-producing goblet cells","Cybrd1, Nqo1, 2210019I11Rik, Gm15816, Vstm2b, Gm13881, Syt8, Tcf23, Nkx6-3, 4930404N11Rik" +"72","Muc6-producing goblet cells","Gkn3, 2310057J18Rik, BC048546, Glp1r, Tff2, Wfdc18, Nkx6-2, Gm16120, Nkx6-3, Kctd14" +"73","Mural cells","Car3, Mylk, Cald1, Flna, Lpl, Prkg1, Limch1, Macf1, Alcam, Sftpc" +"74","Muscle satellite cells","Pax7, Otoa, Gm26834, Megf10, Pdgfrl, Chodl, Rapsn, Myf5, Cdh15, Capn6" +"75","Myelinating Schwann cells","Mpz, Tenm3, Mylk4, Sptbn5, RP23-121N19.3, Gldn, Shc4, Ogn, Ncmap, B230206H07Rik" +"76","Myeloid cells","Itga6, Lims1, Med12l, Timd4, Cd226, Mmp9, Chst11, Gpnmb, Mir99ahg, Gnptab" +"77","Myeloid cells_Alveolar macrophages","Olr1, Ncf1, Cxcl2, Fpr2, Clec7a, Cyb561a3, RP24-443M8.2, Abcg1, Clec4n, Fpr1" +"78","Myeloid cells_Basophils","Rasa3, Dhx40, Hgf, Arhgap10, Il6, Nrgn, Hdc, Nbeal2, Slc6a4, Pim1" +"79","Myeloid cells_Dendritic cells","Aldh1a2, Itgb8, Nr4a3, Slamf7, Col17a1, Wdfy4, Cd80, Il12b, Cd86, Cdk6" +"80","Myeloid cells_Interstitial macrophages","Sirpa, Stab1, Msr1, Ccr5, Nrros, Marco, Aoah, Sdc3, Apobec1, Mrc1" +"81","Myeloid cells_Mast cells","Cpa3, Mcpt1, Tpsb2, Mcpt2, Mcpt9, Olfr920, Mrgprb2, Cd200r3, Mrgprb1, Tpsab1" +"82","Myeloid cells_Monocytes","Hc, Vcan, Fgr, Igsf6, Pot1b, RP23-349H13.2, Sirpb1c, Klra2, Treml4, Gpr141" +"83","Myeloid cells_Neutrophils","Irg1, S100a9, Ncf2, Clec4d, Stfa2l1, R3hdm4, Trem1, A530064D06Rik, RP24-127D13.2, Retnlg" +"84","Myotendinous junction myonuclei","Lama2, Ptprq, Adamts20, Pdlim3, Col22a1, Sim1, Hmgb1-ps8, Gadl1, Kbtbd12, Hephl1" +"85","Ncam1 positive cells","Gm8126, F3, Mir351, C430049B03Rik, Kcnh8, Gm28730, Gm7233, Hoxc4, Wnt16, G6pc2" +"86","Neural cells","Dct, Soat1, Gm12068, Mgll, Slc12a2, Fgl2, Tyr, Zbtb8a, Pax3, Nlrp5-ps" +"87","Neuromuscular junction myonuclei","Prkar1a, Fam19a4, Psd3, Xirp2, Clcn1, Musk, Col19a1, Colq, 2610203C22Rik, Nes" +"88","Ngf positive cells","Angptl2, 2610028E06Rik, Thbs2, Pebp1, Mroh5, Gm20386, Fibin, Ackr4, Tcf21, Plagl1" +"89","Non-myelinating Schwann cells","Spock1, Cdh19, Lrrc4c, Focad, Ptchd4, Pex5l, Cadm2, D7Ertd715e, Col28a1, Dscam" +"90","OB neurons 1","Gm29260, Gm11404, Frmd7, Sp8, Dlx6os2, Sp9, 2900079G21Rik, Grm2, Npffr2, Igfbpl1" +"91","OB neurons 2","Htr1f, Sp8, Trh, Frmd7, Gad2, Sp9, Dlx1, Dlx6, Igfbpl1, Npffr2" +"92","OB neurons 3","Ptprd, Kirrel3, Car10, Reln, Grm8, Nav2, Gabrb1, Fam184a, Kcnh7, Cacnb4" +"93","Oligodendrocyte progenitor cells","Gpr17, Neu4, Zfp488, Olig2, A930009A15Rik, Olig1, Rlbp1, S100a2, AI854517, B9d1os" +"94","Oligodendrocytes","Plp1, Mobp, Prr5l, Cdh20, Mag, Nfasc, Opalin, Ermn, Gm12324, Hapln2" +"95","Osteoblasts","Csmd1, Olfr394, Gm16000, Vmn1r-ps47, Mir694, RP23-456B9.23, Cyp1b1, Vmn2r97, Gm12111, Elane" +"96","Pancreatic acinar cells","Cela1, Pnliprp1, Cel, Cela2a, Cpa2, Cpb1, Pnlip, Cpa1, Galnt6os, Rbpjl" +"97","Paneth cells","Mmp7, Lyz1, Pla2g2a, Itln1, Defa-ps7, Defa-ps4, Mptx2, Gm7861, Gm27162, Gm21498" +"98","Parietal cells","Atp4a, Gm15564, Pla2g1b, Chia1, Tff1, Gkn1, Muc5ac, Gif, Dpcr1, Furin" +"99","Pde4c positive cells","Gm4131, Nkx3-2, Hand1, Tmem200c, RP23-373D16.3, Pde4c, Slc27a6, RP23-291L24.4, Gm26070, Mab21l2" +"100","Pituitary cells","Pomc, Gh, Prl, 4930544I03Rik, Cga, Fshb, Oacyl, Gnrhr, Gm14618, Pou1f1" +"101","Podocytes","Magi2, Podxl, Nphs2, Srgap1, Ptpro, Nphs1, Sema3g, Rhpn1, Wt1os, Gm9946" +"102","Principal cells","Muc20, Klhl14, Ptplad2, Bcam, Muc1, D630044L22Rik, Sesn3, Gstm2, Sbspon, A930017K11Rik" +"103","Proximal tubule cells","Fgf1, Gcnt1, Fut9, Keg1, Lrp2, Slc7a13, Slc6a18, Gm20400, Slc6a15, Sugct" +"104","Pulmonary neuroendocrine cells","Rad51b, Piezo2, Gm12474, Tnfaip2, Colgalt2, Ascl1, Thbs1, Mettl11b, Tcerg1l, Samd1" +"105","Purkinje neurons","Grid2, Anks1b, Itpr1, Cntnap5b, Rgs8, Aldoc, Kcnab1, Arhgef33, Atp1a3, Slc1a6" +"106","Rdh16 positive cells","Dcdc2a, Dnah14, Spag16, Gpr64, Agbl4, Ctnna3, Esr1, Macrod2, Spata16, Nasp" +"107","Secretory cells","Aox1, Bpifa1, 2010007H06Rik, Megf6, Muc5b, Scgb3a1, Gm29455, RP23-227A12.5, Neil2, Gabrp" +"108","Sis positive cells","Nek10, Slc46a1, Gm16054, Pdx1, Hes2, Ltb4r2, Gm15816, Krt12, Otop3, Sphk2" +"109","Skeletal muscle cells","Myh1, Myh8, Rbfox3, Mrvi1, Rxfp1, Mical3, Tnnc2, Ror2, Mb, Tnnt3" +"110","Striatal neurons 1","Pde7b, Gpr88, Pde1b, Drd2, C030005K15Rik, Drd1a, Gpr6, Epyc, Krt9, Gm10754" +"111","Striatal neurons 2","Mir187, Gm13112, Sox1, Gm12665, Prok2, Gm5607, Gm10421, Gm15740, Npy5r, Drd3" +"112","Tenocytes","Col1a1, Col2a1, Col1a2, Sparc, Col11a1, Ibsp, Comp, Col24a1, Chad, Ust" +"113","Thick ascending limb of LOH cells","Egf, Tmem207, Top3b, Cldn16, Gpx6, Gm14002, Gm17225, Tarm1, Nccrp1, 4930461G14Rik" +"114","Tuft cells","Dclk1, Ptbp2, Reg1, St18, Hck, Gnat3, Prap1, Trpm5, Rgs13, Ccnj" +"115","Type A intercalated cells","Oxgr1, 1700028J19Rik, Gm9871, RP24-79E2.3, Tmem61, 1700009J07Rik, 4930563D23Rik, 2410003L11Rik, Rhbg, 2610016A17Rik" +"116","Type B intercalated cells","Car12, Slc26a4, Slc4a9, Gm12121, Insrr, C630028M04Rik, Zcchc16, Hmx2, Atp6v1g3, Gm16353" +"117","Type I alveolar epithelial cells","4930522O17Rik, Pitpnm3, Bik, Gm15809, 2310007B03Rik, Thnsl1, Sorbs3, Wnt3a, Gm16212, Rps14" +"118","Type I myonuclei","Tpm3, Gm10801, Mybpc1, Gm10800, Igfn1, Obscn, Actn2, Frmd4b, Dkk2, Amotl1" +"119","Type II alveolar epithelial cells","C77370, Malt1, Cxcl15, Fam150a, Rmdn2, Gm28856, RP23-23C9.1, RP23-436F15.6, Gm18595, C87198" +"120","Type II myonuclei","Gm26740, Atp2a1, Agbl1, Fbxo32, Ckm, Pdzrn3, Ampd1, Eya4, Mypn, Tbx15" +"121","Unipolar brush cells","Glra2, 9330154J02Rik, RP23-340C13.5, 1700109G14Rik, Gm28652, Cbln1, En2, Gm5089, Gm6030, Gm27008" +"122","Urothelial cells","E230016M11Rik, Snx31, Krt15, Padi1, Gm13219, Upk1a, Olfr890, Phlda3, Upk2, Nipal4" +"123","Vascular endothelial cells","Cacna1c, Airn, Tnnt2, Sorbs2, Rbm20, Ryr2, Mybpc3, Ppm1e, Myom2, Pln" +"124","Vascular endothelial cells_Aerocytes","Gm13816, Gm17158, RP24-74O18.3, Pink1, Gipc3, Gm10287, Gm16564, Zfp697, Prrt4, Begain" +"125","Vascular endothelial cells_General capillary cells","Fcgr2b, Plat, Ackr3, Ecscr, Gm20631, Adcy4, Ankrd63, RP23-462P13.1, Fam71f2, Tmem44" +"126","Vascular leptomeningeal cells","Ptgds, Fndc3c1, Gm6425, Gm17043, Alx3, 2310005E17Rik, Gm12829, Lama1, Gm29521, RP23-340C13.5" +"127","Ventricular cardiomyocytes","Dmd, Cacna1d, Grm1, Zfpm2, D830032E09Rik, Cdh2, Tmtc1, Tlr4, Esrrb, 0610040F04Rik" diff --git a/static/img/references/mousepansciumap.png b/static/img/references/mousepansciumap.png new file mode 100644 index 00000000..14953dac Binary files /dev/null and b/static/img/references/mousepansciumap.png differ