Supplementary Table 1.

The Top 30 Differentially Expressed Genes of Each Cell Type in the dCCA Ecosystem

Gene	p_val	avg_log2FC	pct.1	pct.2	p_val_adj	Cell type
IL7R	0	2.857819907	0.758	0.095	0	T cell
FYN	0	2.248950569	0.962	0.419	0	T cell
BICDL1	0	2.240326143	0.729	0.115	0	T cell
FAAH2	0	2.116057013	0.334	0.087	0	T cell
CAMK4	0	2.074403984	0.668	0.086	0	T cell
STAT4	0	1.990967921	0.845	0.19	0	T cell
BCL11B	0	1.982332052	0.754	0.108	0	T cell
PPP2R5C	0	1.967799479	0.903	0.416	0	T cell
ICOS	0	1.938624088	0.55	0.066	0	T cell
CD96	0	1.914143167	0.762	0.113	0	T cell
PDE3B	0	1.87273318	0.715	0.196	0	T cell
SKAP1	0	1.872352468	0.774	0.156	0	T cell
TRBC2	0	1.852902218	0.708	0.12	0	T cell
CNOT6L	0	1.826390391	0.866	0.382	0	T cell
PTPRC	0	1.813943528	0.973	0.404	0	T cell
CD2	0	1.786055532	0.746	0.098	0	T cell
PBX4	0	1.753179348	0.602	0.088	0	T cell
GZMK	0	1.715931909	0.347	0.034	0	T cell
CD247	0	1.694833662	0.75	0.109	0	T cell
CD3D	0	1.693257118	0.746	0.084	0	T cell
ITK	0	1.676364898	0.598	0.089	0	T cell
TNFAIP3	0	1.676018238	0.876	0.443	0	T cell
PPP1R16B	0	1.66280953	0.769	0.215	0	T cell
RHOH	0	1.66278223	0.802	0.234	0	T cell
CDC42SE2	0	1.660072066	0.942	0.502	0	T cell
TRAC	0	1.642384535	0.646	0.097	0	T cell
THEMIS	0	1.622233359	0.501	0.07	0	T cell
IL32	0	1.610984954	0.78	0.272	0	T cell
CD69	0	1.595429994	0.817	0.253	0	T cell
TRBC1	0	1.581554567	0.45	0.075	0	T cell
KRT17	0	4.534853267	0.453	0.049	0	Epithelial cell
SPINK1	0	4.163811343	0.596	0.061	0	Epithelial cell
KRT19	0	4.080768781	0.825	0.141	0	Epithelial cell
LCN2	0	3.959546363	0.666	0.083	0	Epithelial cell
SCGB3A1	8.06E-128	3.877080534	0.254	0.131	2.60E-123	Epithelial cell
MT1G	0	3.847091868	0.546	0.103	0	Epithelial cell
ERBB2	0	3.608416345	0.563	0.087	0	Epithelial cell
GRB7	0	3.550084194	0.505	0.035	0	Epithelial cell
TFF1	0	3.499223304	0.506	0.037	0	Epithelial cell
TFF3	0	3.407592422	0.545	0.062	0	Epithelial cell
KRT8	0	3.366359295	0.785	0.101	0	Epithelial cell
JUP	0	3.358535225	0.608	0.087	0	Epithelial cell
KRT18	0	3.226750562	0.774	0.112	0	Epithelial cell
PPP1R1B	0	3.18786528	0.508	0.043	0	Epithelial cell
OLFM4	0	3.077164181	0.426	0.041	0	Epithelial cell
ANXA4	0	3.04477107	0.758	0.22	0	Epithelial cell
MT1H	0	3.023401253	0.391	0.042	0	Epithelial cell
MIEN1	0	2.980164106	0.503	0.2	0	Epithelial cell
ELF3	0	2.957400736	0.678	0.06	0	Epithelial cell
CLDN4	0	2.951918348	0.653	0.07	0	Epithelial cell
RPL19	0	2.938058416	0.93	0.893	0	Epithelial cell
GPX2	0	2.937746247	0.614	0.055	0	Epithelial cell
MMP7	0	2.936717406	0.493	0.047	0	Epithelial cell
AGR2	0	2.911912742	0.628	0.059	0	Epithelial cell
LGALS4	0	2.845893248	0.658	0.051	0	Epithelial cell
S100A6	0	2.808406823	0.906	0.761	0	Epithelial cell
PIGR	0	2.738981281	0.403	0.049	0	Epithelial cell
MUC1	0	2.706017595	0.668	0.078	0	Epithelial cell
TM4SF4	0	2.656036851	0.59	0.042	0	Epithelial cell
MUC6	1.02E-108	2.613856486	0.201	0.097	3.30E-104	Epithelial cell
ADAMTS9	0	3.876694139	0.839	0.075	0	Endothelial cell
TCF4	0	3.588912269	0.947	0.176	0	Endothelial cell
ZNF385D	0	3.574882453	0.753	0.035	0	Endothelial cell
VWF	0	3.569547166	0.84	0.048	0	Endothelial cell
MCTP1	0	3.434462613	0.918	0.178	0	Endothelial cell
EMP1	0	3.410764652	0.93	0.218	0	Endothelial cell
ACKR1	0	3.358789683	0.625	0.027	0	Endothelial cell
CALCRL	0	3.307114464	0.874	0.037	0	Endothelial cell
SPARCL1	0	3.266484923	0.937	0.108	0	Endothelial cell
LDB2	0	3.241345019	0.892	0.065	0	Endothelial cell
TM4SF1	0	3.201365489	0.898	0.182	0	Endothelial cell
SLCO2A1	0	3.193838953	0.79	0.024	0	Endothelial cell
COL4A1	0	3.193774373	0.885	0.099	0	Endothelial cell
FLT1	0	3.156215309	0.86	0.064	0	Endothelial cell
SPRY1	0	3.147647502	0.835	0.16	0	Endothelial cell
CCL14	0	3.087868357	0.582	0.028	0	Endothelial cell
A2M	0	3.028232578	0.927	0.168	0	Endothelial cell
AQP1	0	3.018484053	0.814	0.046	0	Endothelial cell
WWTR1	0	2.917536038	0.896	0.134	0	Endothelial cell
RAPGEF4	0	2.913401189	0.824	0.023	0	Endothelial cell
EMCN	0	2.895862599	0.841	0.017	0	Endothelial cell
PLVAP	0	2.894971842	0.82	0.025	0	Endothelial cell
HSPG2	0	2.853125047	0.919	0.162	0	Endothelial cell
SELE	0	2.80142793	0.393	0.015	0	Endothelial cell
COL4A2	0	2.799920879	0.863	0.118	0	Endothelial cell
EPAS1	0	2.774955885	0.916	0.216	0	Endothelial cell
MAGI1	0	2.751448094	0.897	0.151	0	Endothelial cell
ADAMTS1	0	2.719997608	0.696	0.071	0	Endothelial cell
CAV1	0	2.691688397	0.805	0.079	0	Endothelial cell
ADGRL4	0	2.65389204	0.866	0.016	0	Endothelial cell
C1QA	0	3.89063701	0.487	0.027	0	Macrophage
C1QB	0	3.880380561	0.446	0.029	0	Macrophage
HLA-DRA	0	3.627233811	0.973	0.441	0	Macrophage
HLA-DPA1	0	3.567718571	0.896	0.415	0	Macrophage
HLA-DPB1	0	3.425154353	0.878	0.4	0	Macrophage
EREG	0	3.325925957	0.426	0.026	0	Macrophage
C1QC	0	3.162540417	0.41	0.014	0	Macrophage
HLA-DRB1	0	3.104971554	0.94	0.51	0	Macrophage
KYNU	0	3.074751727	0.664	0.047	0	Macrophage
IFI30	0	3.040926899	0.857	0.155	0	Macrophage
HLA-DQA1	0	2.998831628	0.696	0.194	0	Macrophage
APOE	0	2.965012004	0.256	0.058	0	Macrophage
IL1B	0	2.954961415	0.593	0.057	0	Macrophage
HLA-DQB1	0	2.868568236	0.81	0.275	0	Macrophage
HMOX1	0	2.77854088	0.507	0.055	0	Macrophage
CD74	0	2.685857086	0.971	0.653	0	Macrophage
AIF1	0	2.6758084	0.859	0.082	0	Macrophage
HLA-DRB5	0	2.594247645	0.43	0.106	0	Macrophage
FTL	0	2.542025121	0.988	0.915	0	Macrophage
APOC1	0	2.491219299	0.254	0.028	0	Macrophage
LYZ	0	2.443722604	0.848	0.294	0	Macrophage
CTSB	0	2.411376712	0.79	0.304	0	Macrophage
SLC16A10	0	2.401896793	0.383	0.044	0	Macrophage
SELENOP	1.69E-30	2.366839277	0.249	0.187	5.45E-26	Macrophage
CD14	0	2.366292444	0.6	0.054	0	Macrophage
TYROBP	0	2.337370546	0.909	0.161	0	Macrophage
MS4A6A	0	2.337314791	0.677	0.019	0	Macrophage
CCL3	0	2.269957589	0.467	0.089	0	Macrophage
FCER1G	0	2.210063471	0.835	0.12	0	Macrophage
CTSS	0	2.18672832	0.838	0.305	0	Macrophage
S100A8	0	5.135230924	0.883	0.075	0	Neutrophil
G0S2	0	5.015678811	0.88	0.088	0	Neutrophil
CXCL8	0	4.772440753	0.931	0.177	0	Neutrophil
NAMPT	0	4.345599152	0.994	0.606	0	Neutrophil
CCL3L1	0	4.109957587	0.437	0.136	0	Neutrophil
CSF3R	0	4.049324966	0.875	0.059	0	Neutrophil
S100A9	0	3.977599866	0.896	0.109	0	Neutrophil
FCGR3B	0	3.962493007	0.761	0.012	0	Neutrophil
LUCAT1	0	3.927239882	0.773	0.115	0	Neutrophil
AQP9	0	3.90473164	0.72	0.04	0	Neutrophil
PLAUR	0	3.875010777	0.867	0.28	0	Neutrophil
BCL2A1	0	3.794612326	0.864	0.184	0	Neutrophil
C15orf48	0	3.672037458	0.474	0.095	0	Neutrophil
SOD2	0	3.50694026	0.964	0.57	0	Neutrophil
LITAF	0	3.459225875	0.948	0.576	0	Neutrophil
IFITM2	0	3.45718279	0.922	0.596	0	Neutrophil
ALOX5AP	0	3.435853551	0.824	0.265	0	Neutrophil
CCL4L2	8.24E-283	3.428049127	0.473	0.217	2.66E-278	Neutrophil
PLEK	0	3.410378642	0.713	0.149	0	Neutrophil
BASP1	0	3.360817558	0.541	0.143	0	Neutrophil
LCP2	0	3.343282643	0.824	0.295	0	Neutrophil
DOCK4	0	3.295188665	0.816	0.259	0	Neutrophil
ACSL1	0	3.279946864	0.523	0.19	0	Neutrophil
IL1R2	0	3.241952307	0.556	0.047	0	Neutrophil
AZIN1-AS1	0	3.187173586	0.368	0.089	0	Neutrophil
RNF149	0	3.171311295	0.89	0.521	0	Neutrophil
LYN	0	3.154153081	0.803	0.238	0	Neutrophil
LIMK2	0	3.148992449	0.641	0.189	0	Neutrophil
LST1	0	3.147748078	0.734	0.104	0	Neutrophil
PHACTR1	0	3.116701357	0.716	0.186	0	Neutrophil
GNLY	0	3.858558691	0.485	0.042	0	NK cell
GZMB	0	3.293184761	0.726	0.073	0	NK cell
NKG7	0	2.906007893	0.831	0.149	0	NK cell
CCL5	0	2.576973484	0.911	0.262	0	NK cell
CXCL13	0	2.53384098	0.331	0.019	0	NK cell
GZMA	0	2.349490429	0.748	0.15	0	NK cell
KLRC1	0	2.065238897	0.492	0.014	0	NK cell
CCL4	0	2.004697283	0.75	0.221	0	NK cell
IFNG	0	1.939651141	0.576	0.087	0	NK cell
ITGAE	0	1.924947011	0.726	0.195	0	NK cell
TOX	0	1.909817993	0.779	0.212	0	NK cell
CD7	0	1.887301347	0.831	0.215	0	NK cell
ATP8B4	0	1.871117582	0.58	0.059	0	NK cell
PTPN22	0	1.849168772	0.89	0.304	0	NK cell
KLRD1	0	1.843229516	0.641	0.073	0	NK cell
GZMH	0	1.836999377	0.576	0.07	0	NK cell
LINC00299	0	1.824441467	0.577	0.041	0	NK cell
PRF1	0	1.820916776	0.675	0.076	0	NK cell
LINC01871	0	1.765495867	0.693	0.118	0	NK cell
CCL3	0	1.724953556	0.503	0.098	0	NK cell
XCL2	0	1.705719391	0.366	0.046	0	NK cell
AL136456.1	0	1.623449178	0.431	0.103	0	NK cell
RBPJ	0	1.603465772	0.806	0.437	0	NK cell
AC022126.1	0	1.581311541	0.397	0.033	0	NK cell
RGS1	0	1.576108977	0.726	0.282	0	NK cell
CD247	0	1.53503704	0.838	0.297	0	NK cell
HOPX	0	1.531538222	0.573	0.059	0	NK cell
KLRC2	0	1.506351637	0.424	0.013	0	NK cell
CTSW	0	1.485066923	0.538	0.063	0	NK cell
NCALD	0	1.470928648	0.637	0.142	0	NK cell
APOD	0	6.050551093	0.683	0.084	0	Fibroblast
LUM	0	4.888125883	0.834	0.058	0	Fibroblast
DCN	0	4.880080917	0.844	0.073	0	Fibroblast
PTGDS	0	4.771344077	0.55	0.061	0	Fibroblast
SFRP2	0	4.590442556	0.548	0.036	0	Fibroblast
COL1A1	0	4.51645072	0.783	0.105	0	Fibroblast
MGP	0	4.498968329	0.897	0.24	0	Fibroblast
COL3A1	0	4.41673769	0.791	0.08	0	Fibroblast
FBLN1	0	4.308291799	0.752	0.052	0	Fibroblast
COL1A2	0	4.259613198	0.806	0.092	0	Fibroblast
SERPINF1	0	3.75571127	0.725	0.05	0	Fibroblast
CCDC80	0	3.61298915	0.653	0.061	0	Fibroblast
C11orf96	0	3.520053302	0.783	0.147	0	Fibroblast
C1R	0	3.450216085	0.741	0.079	0	Fibroblast
CXCL14	0	3.437706518	0.308	0.015	0	Fibroblast
TIMP1	0	3.392610928	0.92	0.472	0	Fibroblast
CCN1	0	3.374978748	0.745	0.156	0	Fibroblast
CFD	0	3.334867069	0.466	0.078	0	Fibroblast
CCN2	0	3.292721212	0.725	0.14	0	Fibroblast
COL6A2	0	3.174406665	0.791	0.146	0	Fibroblast
C1S	0	3.119602326	0.723	0.105	0	Fibroblast
C7	0	3.097556568	0.578	0.069	0	Fibroblast
C3	0	3.091821258	0.57	0.119	0	Fibroblast
MMP2	0	2.98484368	0.7	0.08	0	Fibroblast
SPARC	0	2.967644036	0.799	0.204	0	Fibroblast
MFAP4	0	2.873302078	0.603	0.025	0	Fibroblast
PLA2G2A	0	2.870107235	0.242	0.014	0	Fibroblast
SFRP4	0	2.828696602	0.402	0.012	0	Fibroblast
COL6A3	0	2.768938434	0.64	0.021	0	Fibroblast
GEM	0	2.73346489	0.63	0.148	0	Fibroblast
IGLC2	0	6.849906924	0.478	0.119	0	B cell
IGKC	0	6.663837129	0.664	0.164	0	B cell
IGHA1	1.96E-291	5.717763579	0.451	0.124	6.31E-287	B cell
IGLC3	0	5.628362435	0.225	0.017	0	B cell
IGHG1	2.33E-280	5.072895022	0.249	0.039	7.52E-276	B cell
IGLC1	1.11E-244	4.402404884	0.173	0.022	3.56E-240	B cell
IGHG3	1.51E-205	4.185434362	0.192	0.031	4.88E-201	B cell
IGHA2	0	4.158321884	0.198	0.02	0	B cell
IGHM	0	3.911990821	0.496	0.013	0	B cell
JCHAIN	0	3.748060975	0.289	0.015	0	B cell
IGHG4	1.68E-77	3.68109683	0.152	0.044	5.42E-73	B cell
IGHG2	0	3.489411077	0.133	0.005	0	B cell
BANK1	0	3.214500103	0.775	0.023	0	B cell
AFF3	0	2.886735796	0.745	0.071	0	B cell
CD79A	0	2.8335787	0.836	0.009	0	B cell
GNG7	0	2.762703066	0.826	0.109	0	B cell
MS4A1	0	2.409367065	0.711	0.015	0	B cell
LY9	0	2.195457745	0.622	0.076	0	B cell
CD83	0	2.190611674	0.816	0.31	0	B cell
RALGPS2	0	2.170996119	0.716	0.126	0	B cell
ARHGAP24	0	2.115798024	0.732	0.147	0	B cell
EBF1	0	2.104186811	0.732	0.158	0	B cell
CD37	0	1.998503761	0.842	0.37	0	B cell
ADAM28	0	1.954540427	0.67	0.087	0	B cell
HLA-DQA1	0	1.881486171	0.814	0.209	0	B cell
ST6GAL1	0	1.841104143	0.744	0.25	0	B cell
CCR7	0	1.758775422	0.609	0.163	0	B cell
BACH2	1.10E-270	1.750314436	0.753	0.361	3.56E-266	B cell
LINC00926	0	1.728629684	0.567	0.012	0	B cell
AC120193.1	0	1.725218641	0.527	0.031	0	B cell
ITGB8	0	4.87318882	0.942	0.086	0	Nerve cell
NRXN1	0	4.768497028	0.915	0.01	0	Nerve cell
PPP2R2B	0	4.75644819	0.926	0.13	0	Nerve cell
CRYAB	0	4.457709408	0.855	0.057	0	Nerve cell
RUNX2	0	4.25276158	0.86	0.187	0	Nerve cell
NAV3	0	4.214723032	0.87	0.1	0	Nerve cell
FRMD5	0	4.161975142	0.892	0.058	0	Nerve cell
STARD13	0	4.138885722	0.926	0.161	0	Nerve cell
TENM3	0	4.063970191	0.886	0.038	0	Nerve cell
CDH19	0	4.019556371	0.883	0.011	0	Nerve cell
EHBP1	0	3.986690914	0.936	0.249	0	Nerve cell
COL8A1	0	3.968060897	0.825	0.031	0	Nerve cell
NRXN3	0	3.836876101	0.868	0.017	0	Nerve cell
GALNT17	0	3.702871986	0.834	0.014	0	Nerve cell
AL139383.1	0	3.593306627	0.808	0.064	0	Nerve cell
CCN3	0	3.532501682	0.714	0.031	0	Nerve cell
GAP43	0	3.439419315	0.811	0.012	0	Nerve cell
ZNF536	0	3.409694843	0.81	0.004	0	Nerve cell
GPM6B	0	3.397168883	0.844	0.057	0	Nerve cell
DST	0	3.318283481	0.935	0.224	0	Nerve cell
SESN3	0	3.30528539	0.837	0.231	0	Nerve cell
ANK3	0	3.212172313	0.933	0.296	0	Nerve cell
CADM2	0	3.060011361	0.696	0.011	0	Nerve cell
SEMA3B	0	3.028846172	0.855	0.075	0	Nerve cell
ADGRB3	0	3.016330199	0.695	0.042	0	Nerve cell
NRP2	0	3.015978753	0.849	0.132	0	Nerve cell
SORCS1	0	2.974886773	0.741	0.018	0	Nerve cell
FN1	0	2.931418143	0.809	0.126	0	Nerve cell
SLC22A23	0	2.928784324	0.673	0.081	0	Nerve cell
ADAMTS9-AS2	0	2.906337313	0.819	0.127	0	Nerve cell
TPSB2	0	6.419787202	0.921	0.029	0	Mast cell
TPSAB1	0	6.085651326	0.914	0.016	0	Mast cell
CPA3	0	4.863626313	0.924	0.005	0	Mast cell
SLC24A3	0	4.092509583	0.938	0.042	0	Mast cell
HPGDS	0	3.848203148	0.878	0.017	0	Mast cell
HPGD	0	2.936250164	0.677	0.067	0	Mast cell
CTSG	0	2.828868123	0.352	0.002	0	Mast cell
MS4A2	0	2.815825714	0.774	0.002	0	Mast cell
HDC	0	2.759363017	0.736	0.006	0	Mast cell
GATA2	0	2.732908987	0.73	0.041	0	Mast cell
FER	0	2.720937805	0.877	0.287	0	Mast cell
AREG	1.36E-214	2.67197275	0.675	0.272	4.38E-210	Mast cell
LTC4S	0	2.607220423	0.655	0.094	0	Mast cell
KIT	0	2.564888405	0.724	0.018	0	Mast cell
ACSL4	0	2.512046759	0.82	0.283	0	Mast cell
SLC18A2	0	2.466939247	0.703	0.024	0	Mast cell
ABCC4	0	2.280137013	0.687	0.126	0	Mast cell
IL1RL1	0	2.221268846	0.713	0.008	0	Mast cell
VWA5A	0	2.217745349	0.649	0.036	0	Mast cell
ADAM12	0	2.193481109	0.645	0.03	0	Mast cell
CSF1	0	2.172964007	0.576	0.113	0	Mast cell
RAB27B	0	2.121452093	0.605	0.037	0	Mast cell
RHEX	0	2.089479665	0.659	0.028	0	Mast cell
ENPP3	0	2.06776375	0.438	0.007	0	Mast cell
IL18R1	0	2.060176401	0.691	0.124	0	Mast cell
ALOX5	0	2.037115764	0.699	0.106	0	Mast cell
RGS13	0	2.016974258	0.672	0.042	0	Mast cell
ANXA1	1.33E-245	1.962156692	0.917	0.598	4.29E-241	Mast cell
CADPS	0	1.939507966	0.531	0.021	0	Mast cell
ADGRE2	0	1.926089903	0.667	0.079	0	Mast cell
TAGLN	0	5.475161646	0.9	0.125	0	Tissue stem cell
ACTA2	0	4.971979812	0.867	0.101	0	Tissue stem cell
C11orf96	0	4.518464263	0.912	0.161	0	Tissue stem cell
MYL9	0	4.290246475	0.917	0.125	0	Tissue stem cell
TPM2	0	4.187163834	0.906	0.13	0	Tissue stem cell
MYH11	0	4.084321297	0.741	0.058	0	Tissue stem cell
ADIRF	0	3.903358852	0.902	0.153	0	Tissue stem cell
RGS5	0	3.569655911	0.499	0.031	0	Tissue stem cell
MUSTN1	0	3.482426649	0.659	0.011	0	Tissue stem cell
CRISPLD2	0	3.457782966	0.805	0.076	0	Tissue stem cell
PRKG1	0	3.409746635	0.844	0.117	0	Tissue stem cell
CALD1	0	3.409170838	0.942	0.227	0	Tissue stem cell
SOD3	0	3.226520727	0.808	0.043	0	Tissue stem cell
IGFBP7	0	3.124695849	0.96	0.296	0	Tissue stem cell
DSTN	0	3.113584738	0.927	0.441	0	Tissue stem cell
SPARCL1	0	2.970323941	0.908	0.194	0	Tissue stem cell
TPM1	0	2.95328782	0.851	0.22	0	Tissue stem cell
CSRP2	0	2.871080931	0.802	0.064	0	Tissue stem cell
PPP1R14A	0	2.85268515	0.791	0.036	0	Tissue stem cell
PDK4	0	2.828109884	0.666	0.122	0	Tissue stem cell
MFGE8	0	2.66823482	0.817	0.088	0	Tissue stem cell
PDE3A	0	2.660932195	0.759	0.042	0	Tissue stem cell
NDUFA4L2	0	2.627323903	0.539	0.01	0	Tissue stem cell
NOTCH3	0	2.576897674	0.814	0.025	0	Tissue stem cell
PDGFRB	0	2.565128239	0.763	0.038	0	Tissue stem cell
SOX5	0	2.550861642	0.788	0.111	0	Tissue stem cell
CEBPD	0	2.53665668	0.842	0.251	0	Tissue stem cell
RERGL	0	2.526515505	0.52	0.007	0	Tissue stem cell
SORBS2	0	2.496744624	0.624	0.106	0	Tissue stem cell
CSRP1	0	2.469935441	0.747	0.19	0	Tissue stem cell

dCCA, Distal cholangiocarcinoma.