pbmc_1k_v2 — Cell Ranger

Shown here are the total UMI counts for each cell-barcode. Cells with greater UMI counts likely have higher RNA content than cells with fewer UMI counts. The axes correspond to the 2-dimensional embedding produced by the t-SNE algorithm. In this space, pairs of cells that are close to each other have more similar gene expression profiles than cells that are distant from each other. The display is limited to a random subset of 10000 cells.

t-SNE Projection of Cells Colored by UMI Counts

These are the assignments of each cell-barcode a clusters by an automated clustering algorithm. The clustering groups together cells that have similar expression profiles. The axes correspond to the 2-dimensional embedding produced by the t-SNE algorithm. In this space, pairs of cells that are close to each other have more similar gene expression profiles than cells that are distant from each other. The display is limited to a random subset of 10000 cells and K-means up to K=20. Please use Loupe(tm) Cell Browser to view the entire dataset.

t-SNE projection of Cells Colored by Automated Clustering

The differential expression analysis seeks to find, for each cluster, genes that are more highly expressed in that cluster relative to the rest of the sample. Here a differential expression test was performed between each cluster and the rest of the sample for each gene. The Log2 fold-change (L2FC) is an estimate of the log2 ratio of expression in a cluster to that in all other cells. A value of 1.0 indicates 2-fold greater expression in the cluster of interest. The p-value is a measure of the statistical significance of the expression difference and is based on a negative binomial test. The p-value reported here has been adjusted for multiple testing via the Benjamini-Hochberg procedure. In this table you can click on a column to sort by that value. Also, in this table genes were filtered by (Mean UMI counts > 1.0) and the top N genes by L2FC for each cluster were retained. Genes with L2FC < 0 or adjusted p-value >= 0.10 were grayed out. The number of top genes shown per cluster, N, is set to limit the number of table entries shown to 10000; N=10000/K^2 where K is the number of clusters. N can range from 1 to 50. For the full table, please refer to the "differential_expression.csv" files produced by the pipeline.

Top Genes By Cluster (Log2 fold-change, p-value)

Gene ID	Gene name	L2FC	p-value	L2FC	p-value	L2FC	p-value	L2FC	p-value	L2FC	p-value
		Cluster 1		Cluster 2		Cluster 3		Cluster 4		Cluster 5
ENSG00000168685	IL7R	1.85	4e-07	1.22	6e-03	-4.31	1e-14	-4.57	1e-05	-5.84	5e-09
ENSG00000142546	NOSIP	1.83	9e-08	0.50	5e-01	-2.05	7e-06	-1.99	4e-02	-2.25	4e-03
ENSG00000198851	CD3E	1.66	1e-06	1.43	1e-04	-4.69	1e-18	-4.63	1e-06	-5.63	2e-10
ENSG00000211751	TRBC1	1.64	1e-05	1.44	5e-04	-4.86	1e-16	-4.19	4e-05	-6.04	2e-09
ENSG00000111716	LDHB	1.63	7e-07	0.40	6e-01	-1.57	3e-04	-1.79	5e-02	-1.70	3e-02
ENSG00000277734	TRAC	1.61	5e-06	1.48	9e-05	-5.53	2e-22	-4.75	5e-07	-4.23	5e-08
ENSG00000167286	CD3D	1.45	5e-05	1.65	5e-06	-4.98	7e-20	-5.13	2e-07	-5.81	9e-11
ENSG00000211772	TRBC2	1.37	2e-04	1.41	3e-04	-4.60	9e-18	-4.56	2e-06	-1.36	2e-01
ENSG00000204387	C6orf48	1.22	8e-04	-0.47	6e-01	-0.92	8e-02	-1.53	1e-01	0.39	9e-01
ENSG00000182866	LCK	1.09	6e-03	1.87	1e-07	-4.46	2e-16	-3.56	1e-04	-3.03	8e-05
ENSG00000152558	TMEM123	1.09	5e-03	-0.01	1e+00	-1.14	2e-02	-0.36	1e+00	-0.29	1e+00
ENSG00000213741	RPS29	1.07	3e-03	0.09	1e+00	-1.21	3e-03	-1.64	3e-02	0.27	1e+00
ENSG00000071082	RPL31	1.00	7e-03	0.12	1e+00	-1.02	2e-02	-1.46	1e-01	0.10	1e+00
ENSG00000118181	RPS25	0.98	9e-03	0.06	1e+00	-1.06	1e-02	-1.33	2e-01	0.23	1e+00
ENSG00000137154	RPS6	0.98	9e-03	-0.13	1e+00	-0.82	8e-02	-1.28	1e-01	0.23	1e+00
ENSG00000112306	RPS12	0.93	1e-02	-0.05	1e+00	-0.70	2e-01	-1.01	3e-01	-0.04	1e+00
ENSG00000181163	NPM1	0.92	2e-02	0.05	1e+00	-0.74	2e-01	-1.19	3e-01	-0.05	1e+00
ENSG00000149273	RPS3	0.91	2e-02	0.25	8e-01	-0.97	3e-02	-1.46	1e-01	0.03	1e+00
ENSG00000177954	RPS27	0.91	2e-02	-0.01	1e+00	-1.13	7e-03	-1.24	2e-01	0.49	8e-01
ENSG00000072818	ACAP1	0.90	4e-02	1.14	7e-03	-2.68	1e-08	-3.18	5e-04	0.07	1e+00
ENSG00000105373	NOP53	0.90	2e-02	0.03	1e+00	-1.03	3e-02	-1.65	6e-02	0.50	7e-01
ENSG00000156482	RPL30	0.89	2e-02	-0.11	1e+00	-0.83	8e-02	-1.21	3e-01	0.35	1e+00
ENSG00000100316	RPL3	0.88	2e-02	0.20	9e-01	-0.98	3e-02	-1.51	9e-02	0.21	1e+00
ENSG00000227507	LTB	0.87	5e-02	0.67	2e-01	-3.49	7e-15	-4.22	5e-07	1.09	7e-02
ENSG00000266402	SNHG25	0.87	4e-02	-0.27	9e-01	-0.32	8e-01	-0.24	1e+00	-0.66	9e-01
ENSG00000174444	RPL4	0.82	4e-02	-0.10	1e+00	-0.60	3e-01	-1.37	2e-01	0.26	1e+00
ENSG00000114942	EEF1B2	0.80	6e-02	-0.19	1e+00	-0.63	3e-01	-1.60	7e-02	0.51	7e-01
ENSG00000133872	SARAF	0.80	5e-02	0.24	8e-01	-0.64	3e-01	-0.46	1e+00	-0.77	7e-01
ENSG00000198242	RPL23A	0.80	5e-02	0.17	9e-01	-1.07	1e-02	-1.68	5e-02	0.51	7e-01
ENSG00000008988	RPS20	0.79	6e-02	-0.02	1e+00	-0.77	1e-01	-1.32	2e-01	0.39	9e-01
ENSG00000130255	RPL36	0.76	7e-02	-0.15	1e+00	-0.56	3e-01	-0.72	6e-01	0.11	1e+00
ENSG00000171858	RPS21	0.76	7e-02	0.00	1e+00	-0.75	1e-01	-1.17	3e-01	0.35	1e+00
ENSG00000177600	RPLP2	0.76	7e-02	-0.14	1e+00	-0.66	2e-01	-0.94	4e-01	0.34	1e+00
ENSG00000164587	RPS14	0.76	7e-02	-0.03	1e+00	-0.53	4e-01	-0.65	7e-01	-0.14	1e+00
ENSG00000168028	RPSA	0.75	9e-02	0.27	8e-01	-1.06	2e-02	-2.30	3e-03	0.59	6e-01
ENSG00000143947	RPS27A	0.75	8e-02	0.00	1e+00	-0.77	1e-01	-0.84	5e-01	0.25	1e+00
ENSG00000231500	RPS18	0.74	8e-02	0.01	1e+00	-0.72	2e-01	-1.11	3e-01	0.30	1e+00
ENSG00000122406	RPL5	0.74	9e-02	0.12	1e+00	-0.63	3e-01	-1.46	1e-01	0.17	1e+00
ENSG00000196683	TOMM7	0.74	9e-02	-0.20	1e+00	-0.44	6e-01	-0.43	1e+00	-0.13	1e+00
ENSG00000172809	RPL38	0.74	9e-02	-0.12	1e+00	-0.55	4e-01	-0.79	7e-01	0.14	1e+00
ENSG00000108298	RPL19	0.74	9e-02	-0.07	1e+00	-0.57	3e-01	-1.24	2e-01	0.29	1e+00
ENSG00000134419	RPS15A	0.74	9e-02	-0.13	1e+00	-0.55	4e-01	-0.59	8e-01	0.04	1e+00
ENSG00000179144	GIMAP7	0.73	1e-01	1.37	4e-04	-1.23	1e-02	-1.12	4e-01	-6.07	8e-11
ENSG00000105193	RPS16	0.73	1e-01	-0.12	1e+00	-0.52	4e-01	-0.97	5e-01	0.21	1e+00
ENSG00000167526	RPL13	0.73	9e-02	-0.13	1e+00	-0.69	2e-01	-0.76	6e-01	0.33	1e+00
ENSG00000182899	RPL35A	0.72	1e-01	-0.07	1e+00	-0.64	2e-01	-0.69	7e-01	0.16	1e+00
ENSG00000104408	EIF3E	0.72	1e-01	-0.28	9e-01	-0.40	7e-01	-0.27	1e+00	-0.14	1e+00
ENSG00000109971	HSPA8	0.72	1e-01	0.85	6e-02	-0.88	9e-02	-2.36	4e-03	-0.62	9e-01
ENSG00000196405	EVL	0.71	1e-01	1.24	1e-03	-1.99	4e-06	-4.09	4e-06	-0.07	1e+00
ENSG00000144713	RPL32	0.70	1e-01	-0.31	8e-01	-0.44	6e-01	-0.56	8e-01	0.18	1e+00
ENSG00000233927	RPS28	0.70	1e-01	-0.14	1e+00	-0.53	4e-01	-0.70	7e-01	0.16	1e+00
ENSG00000083845	RPS5	0.69	1e-01	-0.13	1e+00	-0.74	1e-01	-1.38	1e-01	0.67	5e-01
ENSG00000104964	AES	0.69	2e-01	1.27	9e-04	-2.26	2e-07	-2.62	2e-03	-0.08	1e+00
ENSG00000133321	RARRES3	0.64	2e-01	1.66	7e-06	-1.63	6e-04	-2.34	1e-02	-2.41	2e-03
ENSG00000008517	IL32	0.60	3e-01	2.49	5e-14	-4.92	4e-21	-4.96	1e-07	-6.80	9e-14
ENSG00000172183	ISG20	0.59	3e-01	0.54	4e-01	-3.17	3e-10	-4.05	5e-05	1.55	1e-03
ENSG00000173762	CD7	0.56	4e-01	2.45	2e-11	-4.29	2e-14	-5.26	2e-06	-3.63	2e-05
ENSG00000156976	EIF4A2	0.49	4e-01	0.20	9e-01	-1.03	3e-02	-0.94	5e-01	0.72	4e-01
ENSG00000167658	EEF2	0.42	5e-01	-0.02	1e+00	-0.49	5e-01	-1.21	3e-01	0.66	4e-01
ENSG00000198821	CD247	0.42	7e-01	2.61	7e-12	-4.29	5e-12	-4.75	9e-05	-4.00	4e-05
ENSG00000105640	RPL18A	0.41	5e-01	-0.25	9e-01	-0.41	6e-01	-0.65	7e-01	0.61	6e-01
ENSG00000188404	SELL	0.41	6e-01	-0.46	6e-01	-1.18	2e-02	0.13	1e+00	1.10	6e-02
ENSG00000132424	PNISR	0.28	8e-01	0.07	1e+00	-0.85	1e-01	-0.74	8e-01	0.94	1e-01
ENSG00000175463	TBC1D10C	0.25	8e-01	1.26	2e-03	-1.65	4e-04	-2.22	2e-02	0.31	1e+00
ENSG00000096384	HSP90AB1	0.24	8e-01	0.34	6e-01	-0.64	3e-01	-1.23	3e-01	0.65	5e-01
ENSG00000131508	UBE2D2	0.11	1e+00	0.03	1e+00	-0.58	4e-01	-0.74	8e-01	0.96	1e-01
ENSG00000147168	IL2RG	0.07	1e+00	1.73	2e-06	-2.16	4e-06	-3.18	6e-04	0.17	1e+00
ENSG00000136490	LIMD2	0.03	1e+00	0.03	1e+00	-0.31	8e-01	-1.08	4e-01	0.89	2e-01
ENSG00000197540	GZMM	0.01	1e+00	3.05	4e-16	-4.75	3e-13	-3.79	8e-04	-6.06	2e-07
ENSG00000198668	CALM1	-0.00	1e+00	1.26	7e-04	-0.86	1e-01	-0.78	7e-01	-0.67	8e-01
ENSG00000142534	RPS11	-0.05	1e+00	-0.44	6e-01	0.10	1e+00	-0.32	1e+00	0.65	5e-01
ENSG00000110934	BIN2	-0.06	1e+00	1.52	8e-05	-0.71	3e-01	-1.63	1e-01	-1.08	4e-01
ENSG00000160932	LY6E	-0.09	1e+00	1.22	2e-03	-0.37	8e-01	-3.62	6e-05	-0.29	1e+00
ENSG00000112576	CCND3	-0.09	1e+00	1.22	3e-03	-0.79	2e-01	-0.84	7e-01	-0.39	1e+00
ENSG00000008952	SEC62	-0.10	1e+00	-0.04	1e+00	-0.63	4e-01	-0.30	1e+00	1.13	5e-02
ENSG00000128340	RAC2	-0.12	1e+00	1.33	3e-04	-0.81	1e-01	-1.25	3e-01	-0.40	1e+00
ENSG00000121966	CXCR4	-0.15	1e+00	0.05	1e+00	-1.88	1e-04	-0.80	8e-01	1.96	2e-05
ENSG00000101608	MYL12A	-0.19	1e+00	1.02	1e-02	-0.54	4e-01	-0.20	1e+00	-0.69	8e-01
ENSG00000092010	PSME1	-0.19	1e+00	1.02	1e-02	-0.45	6e-01	-0.50	1e+00	-0.54	1e+00
ENSG00000206503	HLA-A	-0.22	9e-01	1.30	4e-04	-0.68	2e-01	-1.09	4e-01	-0.43	1e+00
ENSG00000162511	LAPTM5	-0.23	9e-01	-0.25	9e-01	-0.21	1e+00	-0.39	1e+00	1.07	4e-02
ENSG00000169442	CD52	-0.35	7e-01	0.07	1e+00	-0.21	9e-01	-0.55	1e+00	0.95	1e-01
ENSG00000204525	HLA-C	-0.36	7e-01	1.18	2e-03	-0.36	7e-01	-1.05	4e-01	-0.43	1e+00
ENSG00000157514	TSC22D3	-0.41	7e-01	-0.29	9e-01	-0.15	1e+00	0.47	8e-01	0.74	4e-01
ENSG00000234745	HLA-B	-0.41	6e-01	1.03	1e-02	-0.30	8e-01	-0.86	6e-01	-0.19	1e+00
ENSG00000170315	UBB	-0.43	7e-01	1.37	2e-04	-0.91	7e-02	-1.51	1e-01	0.26	1e+00
ENSG00000002586	CD99	-0.49	6e-01	1.43	2e-04	-0.37	8e-01	-0.68	9e-01	-1.19	3e-01
ENSG00000175567	UCP2	-0.54	5e-01	0.39	6e-01	0.05	1e+00	-1.18	4e-01	0.72	4e-01
ENSG00000166794	PPIB	-0.62	4e-01	1.07	1e-02	-0.06	1e+00	-0.95	6e-01	-0.28	1e+00
ENSG00000240065	PSMB9	-0.66	3e-01	1.07	1e-02	-0.07	1e+00	-1.11	4e-01	-0.14	1e+00
ENSG00000126264	HCST	-0.66	3e-01	1.57	8e-06	-0.24	9e-01	-0.25	1e+00	-3.40	1e-06
ENSG00000185201	IFITM2	-0.79	2e-01	1.31	7e-04	0.20	9e-01	-1.00	5e-01	-1.50	1e-01
ENSG00000104894	CD37	-0.80	2e-01	-0.73	3e-01	-0.42	7e-01	-0.72	8e-01	2.12	8e-08
ENSG00000143384	MCL1	-0.97	8e-02	-0.68	4e-01	0.58	3e-01	1.84	2e-04	-2.18	6e-03
ENSG00000143119	CD53	-1.17	2e-02	0.68	2e-01	-0.27	9e-01	0.02	1e+00	0.73	4e-01
ENSG00000111796	KLRB1	-1.34	2e-02	4.26	6e-31	-4.54	5e-15	-4.21	7e-05	-6.06	2e-09
ENSG00000197006	METTL9	-1.37	8e-03	-0.83	3e-01	0.40	6e-01	2.21	3e-06	-1.50	1e-01
ENSG00000130522	JUND	-1.44	6e-03	-1.22	5e-02	0.98	3e-02	1.89	2e-04	-1.80	6e-02
ENSG00000112335	SNX3	-1.52	7e-04	-0.97	1e-01	0.78	7e-02	0.66	5e-01	0.84	2e-01
ENSG00000137575	SDCBP	-1.57	1e-03	-1.14	6e-02	1.07	8e-03	1.77	4e-04	-1.57	1e-01
ENSG00000158517	NCF1	-1.58	1e-03	-1.74	1e-03	-0.16	1e+00	1.65	2e-03	1.46	4e-03
ENSG00000160255	ITGB2	-1.64	2e-04	1.05	1e-02	0.59	2e-01	0.23	1e+00	-2.01	6e-03
ENSG00000172543	CTSW	-1.65	3e-03	4.29	2e-30	-3.16	9e-09	-4.65	5e-05	-6.92	4e-09
ENSG00000266412	NCOA4	-1.76	2e-01	-0.85	8e-01	0.48	8e-01	2.30	2e-02	-1.37	1e+00
ENSG00000271503	CCL5	-1.89	2e-03	3.84	2e-21	-3.23	5e-08	-0.91	9e-01	-5.59	3e-07
ENSG00000167996	FTH1	-1.91	3e-06	-1.78	9e-05	1.94	2e-09	0.90	2e-01	-1.16	2e-01
ENSG00000042753	AP2S1	-1.92	3e-05	-1.12	6e-02	1.64	2e-06	1.22	4e-02	-1.75	4e-02
ENSG00000140575	IQGAP1	-1.97	5e-05	-0.85	3e-01	1.03	1e-02	1.62	3e-03	-0.81	7e-01
ENSG00000243449	C4orf48	-1.97	5e-05	-1.24	4e-02	1.28	1e-03	1.61	3e-03	-1.04	5e-01
ENSG00000213719	CLIC1	-1.99	3e-06	0.95	3e-02	0.29	7e-01	0.05	1e+00	0.03	1e+00
ENSG00000103187	COTL1	-2.01	3e-06	-1.67	7e-04	2.30	9e-13	0.45	8e-01	-1.58	6e-02
ENSG00000163931	TKT	-2.03	7e-06	-1.78	6e-04	1.83	8e-08	1.20	5e-02	-1.29	2e-01
ENSG00000136238	RAC1	-2.05	2e-06	-1.17	4e-02	1.70	4e-07	1.25	3e-02	-1.95	1e-02
ENSG00000172216	CEBPB	-2.10	8e-06	-1.83	6e-04	2.07	2e-09	1.04	1e-01	-1.77	5e-02
ENSG00000130313	PGLS	-2.12	8e-06	-1.10	8e-02	1.85	1e-07	0.81	4e-01	-1.16	4e-01
ENSG00000117984	CTSD	-2.14	5e-06	-0.19	1e+00	0.84	6e-02	1.88	1e-04	-3.40	2e-05
ENSG00000187118	CMC1	-2.22	3e-03	4.33	3e-19	-3.03	4e-05	-2.99	7e-02	-2.76	6e-02
ENSG00000170345	FOS	-2.24	2e-07	-2.05	2e-05	1.23	9e-04	2.24	6e-07	-2.09	4e-03
ENSG00000142347	MYO1F	-2.28	3e-06	1.49	2e-04	0.59	3e-01	-0.23	1e+00	-2.25	8e-03
ENSG00000205302	SNX2	-2.30	4e-06	-1.51	1e-02	0.54	4e-01	-0.11	1e+00	2.14	7e-07
ENSG00000120129	DUSP1	-2.30	5e-08	-1.38	7e-03	1.15	2e-03	1.89	6e-05	-1.00	5e-01
ENSG00000104870	FCGRT	-2.30	2e-06	-3.02	6e-08	2.37	1e-11	1.19	7e-02	-2.32	6e-03
ENSG00000130066	SAT1	-2.31	1e-07	-1.23	3e-02	1.84	6e-08	1.21	4e-02	-2.15	4e-03
ENSG00000197956	S100A6	-2.31	3e-08	-1.29	1e-02	1.62	1e-06	1.63	9e-04	-2.92	1e-05
ENSG00000245532	NEAT1	-2.39	2e-08	-1.25	2e-02	1.63	2e-06	1.60	2e-03	-2.66	1e-04
ENSG00000103490	PYCARD	-2.42	1e-07	-1.35	1e-02	1.92	1e-08	1.04	1e-01	-1.40	1e-01
ENSG00000163191	S100A11	-2.44	2e-08	-0.96	1e-01	1.86	2e-08	1.25	3e-02	-3.76	2e-07
ENSG00000164111	ANXA5	-2.50	3e-07	-1.38	2e-02	1.94	4e-08	1.17	8e-02	-1.69	7e-02
ENSG00000111144	LTA4H	-2.50	1e-07	-2.20	3e-05	1.40	2e-04	1.58	3e-03	-0.06	1e+00
ENSG00000087086	FTL	-2.58	2e-10	-2.54	1e-08	1.99	5e-10	1.51	4e-03	-1.69	2e-02
ENSG00000182718	ANXA2	-2.66	5e-09	-0.21	1e+00	1.93	8e-09	0.03	1e+00	-1.45	1e-01
ENSG00000084207	GSTP1	-2.68	8e-10	-0.88	2e-01	1.86	2e-08	1.02	1e-01	-1.78	2e-02
ENSG00000104763	ASAH1	-2.71	1e-08	-1.51	6e-03	1.79	3e-07	1.46	8e-03	-1.57	9e-02
ENSG00000182287	AP1S2	-2.79	1e-09	-2.75	5e-08	1.91	2e-08	1.80	2e-04	-2.20	5e-03
ENSG00000171476	HOPX	-2.80	6e-06	4.52	9e-27	-4.12	1e-09	-3.75	4e-03	-1.35	5e-01
ENSG00000122862	SRGN	-2.86	9e-11	-0.49	6e-01	1.10	5e-03	2.01	1e-05	-4.17	1e-08
ENSG00000119655	NPC2	-2.88	3e-10	-3.28	1e-10	2.17	7e-11	1.21	4e-02	-0.71	8e-01
ENSG00000122986	HVCN1	-2.90	6e-06	-3.63	1e-06	-0.84	3e-01	-0.70	1e+00	4.01	1e-19
ENSG00000145649	GZMA	-2.94	1e-07	5.22	3e-39	-3.41	3e-09	-5.60	1e-05	-4.85	2e-06
ENSG00000077984	CST7	-2.95	1e-06	5.44	8e-37	-4.24	1e-10	-4.02	2e-03	-4.69	3e-05
ENSG00000204472	AIF1	-3.24	5e-12	-5.15	3e-19	2.76	1e-16	1.38	2e-02	-8.47	2e-15
ENSG00000076944	STXBP2	-3.33	6e-11	-2.41	1e-05	1.71	4e-06	2.18	8e-06	-3.48	3e-05
ENSG00000197746	PSAP	-3.36	1e-13	-2.42	5e-07	2.39	1e-13	1.28	2e-02	-2.35	1e-03
ENSG00000126759	CFP	-3.42	3e-10	-4.47	1e-11	2.71	3e-14	1.43	2e-02	-4.47	3e-06
ENSG00000084234	APLP2	-3.47	9e-11	-2.89	3e-07	1.28	1e-03	2.19	6e-06	-0.30	1e+00
ENSG00000090013	BLVRB	-3.49	4e-10	-3.19	1e-07	1.89	5e-07	2.15	2e-05	-3.09	6e-04
ENSG00000197766	CFD	-3.62	3e-11	-5.53	6e-15	2.73	2e-14	1.46	2e-02	-3.92	1e-05
ENSG00000204257	HLA-DMA	-3.76	3e-12	-2.85	3e-07	1.70	4e-06	-0.67	9e-01	1.71	3e-04
ENSG00000115271	GCA	-3.77	2e-10	-3.47	6e-08	1.13	1e-02	2.57	1e-07	-0.57	1e+00
ENSG00000163131	CTSS	-3.79	2e-16	-3.55	6e-13	1.91	1e-08	2.01	2e-05	-1.78	3e-02
ENSG00000025708	TYMP	-3.89	2e-15	-2.90	1e-08	2.35	2e-12	1.56	3e-03	-2.58	7e-04
ENSG00000116741	RGS2	-3.91	6e-12	-2.46	3e-05	1.09	2e-02	2.88	1e-09	-3.05	8e-04
ENSG00000030582	GRN	-4.10	8e-15	-4.07	1e-12	2.52	2e-13	1.53	6e-03	-2.43	3e-03
ENSG00000180644	PRF1	-4.14	4e-09	6.46	3e-39	-4.28	2e-09	-5.91	2e-04	-6.17	8e-06
ENSG00000007312	CD79B	-4.17	1e-11	-2.57	4e-05	-2.18	9e-05	-6.32	6e-06	5.39	1e-39
ENSG00000134539	KLRD1	-4.17	2e-07	6.22	8e-31	-3.73	2e-06	-5.21	3e-03	-5.47	4e-04
ENSG00000113269	RNF130	-4.18	6e-14	-2.38	1e-05	2.21	3e-10	1.69	1e-03	-2.87	6e-04
ENSG00000102524	TNFSF13B	-4.27	3e-11	-3.74	3e-08	1.83	5e-06	2.35	4e-06	-2.96	3e-03
ENSG00000242574	HLA-DMB	-4.36	3e-13	-3.35	3e-08	1.24	3e-03	-0.62	1e+00	2.32	1e-07
ENSG00000019582	CD74	-4.55	3e-21	-3.11	2e-10	1.01	2e-02	-1.57	1e-01	2.70	3e-12
ENSG00000136826	KLF4	-4.56	4e-13	-6.09	5e-14	1.79	6e-06	2.59	1e-07	-5.07	2e-06
ENSG00000100097	LGALS1	-4.63	4e-22	-2.35	8e-07	2.15	6e-11	1.84	2e-04	-4.30	3e-09
ENSG00000143878	RHOB	-4.64	8e-14	-3.62	8e-09	1.67	3e-05	2.46	8e-07	-2.40	1e-02
ENSG00000105374	NKG7	-4.79	1e-14	6.11	2e-49	-3.64	6e-10	-4.90	4e-05	-6.17	1e-08
ENSG00000105369	CD79A	-4.88	2e-13	-4.41	3e-10	-5.87	2e-15	-5.32	5e-05	7.73	1e-63
ENSG00000204482	LST1	-4.91	3e-21	-4.03	4e-14	2.89	5e-18	1.31	3e-02	-4.25	4e-08
ENSG00000140968	IRF8	-4.97	2e-11	-3.18	7e-06	1.18	2e-02	-0.49	1e+00	2.37	3e-06
ENSG00000170458	CD14	-5.08	2e-12	-4.78	6e-10	1.64	2e-04	2.73	1e-07	-4.78	3e-05
ENSG00000211829	TRDC	-5.22	8e-09	6.13	5e-29	-3.16	5e-05	-5.24	5e-03	-5.50	5e-04
ENSG00000135218	CD36	-5.32	9e-15	-6.02	8e-14	1.71	2e-05	2.72	2e-08	-6.01	3e-07
ENSG00000223865	HLA-DPB1	-5.40	1e-23	-3.57	7e-12	1.98	2e-08	-1.53	2e-01	1.79	8e-05
ENSG00000211679	IGLC3	-5.55	6e-03	-6.25	1e-02	-6.54	2e-03	-3.97	1e+00	9.16	1e-15
ENSG00000115523	GNLY	-5.57	3e-14	5.95	2e-38	-3.05	4e-06	-6.53	2e-05	-6.47	3e-07
ENSG00000121316	PLBD1	-5.58	5e-11	-5.28	7e-09	1.41	5e-03	3.03	3e-08	-5.27	9e-05
ENSG00000129226	CD68	-5.61	6e-17	-4.99	5e-13	3.05	5e-17	1.24	7e-02	-3.48	1e-04
ENSG00000127920	GNG11	-5.66	3e-02	-3.76	3e-01	-1.48	8e-01	5.77	5e-06	-4.35	1e+00
ENSG00000224397	SMIM25	-5.68	2e-13	-5.38	7e-11	3.23	6e-15	1.18	2e-01	-5.96	3e-06
ENSG00000163737	PF4	-5.81	2e-02	-5.51	9e-02	-2.73	4e-01	7.03	2e-08	-5.50	9e-01
ENSG00000143546	S100A8	-5.88	9e-26	-6.62	1e-25	0.85	9e-02	3.56	1e-16	-6.34	8e-13
ENSG00000158869	FCER1G	-5.89	1e-26	-0.87	2e-01	2.29	3e-12	1.06	1e-01	-3.85	2e-07
ENSG00000128218	VPREB3	-5.92	6e-09	-5.62	3e-07	-5.90	8e-09	-3.34	6e-02	9.12	5e-42
ENSG00000110077	MS4A6A	-5.94	3e-20	-5.64	2e-16	2.00	4e-08	2.40	4e-07	-4.62	3e-07
ENSG00000100079	LGALS2	-5.96	9e-19	-7.67	2e-18	2.92	6e-16	1.53	1e-02	-6.65	4e-09
ENSG00000153064	BANK1	-6.01	6e-10	-4.70	4e-07	-3.37	4e-06	-3.43	2e-02	7.16	3e-40
ENSG00000247982	LINC00926	-6.09	1e-09	-5.78	8e-08	-4.47	1e-07	-4.51	8e-03	8.69	1e-43
ENSG00000196735	HLA-DQA1	-6.12	3e-17	-4.82	4e-12	0.99	4e-02	-3.81	6e-04	3.12	1e-13
ENSG00000179344	HLA-DQB1	-6.16	6e-20	-4.04	3e-11	1.11	1e-02	-1.63	2e-01	2.78	2e-11
ENSG00000081189	MEF2C	-6.19	1e-18	-4.46	4e-12	0.77	1e-01	0.79	4e-01	2.34	8e-08
ENSG00000165168	CYBB	-6.19	1e-16	-5.89	1e-13	1.88	9e-07	2.20	1e-05	-1.08	5e-01
ENSG00000066336	SPI1	-6.21	5e-22	-5.59	2e-17	2.91	9e-18	1.14	8e-02	-1.59	1e-01
ENSG00000211899	IGHM	-6.22	1e-18	-5.07	1e-12	-5.00	2e-14	-6.39	2e-06	8.05	2e-70
ENSG00000156738	MS4A1	-6.28	6e-14	-4.97	8e-10	-6.26	1e-13	-5.71	1e-04	8.89	3e-61
ENSG00000237541	HLA-DQA2	-6.37	7e-18	-4.74	3e-12	1.83	1e-06	-2.18	5e-02	2.18	1e-06
ENSG00000011600	TYROBP	-6.40	7e-33	-1.67	7e-04	2.05	4e-10	1.85	1e-04	-5.78	1e-13
ENSG00000163221	S100A12	-6.42	1e-24	-7.22	3e-23	0.83	1e-01	3.61	2e-16	-7.02	6e-12
ENSG00000231389	HLA-DPA1	-6.44	1e-27	-3.69	3e-12	2.07	5e-09	-1.78	1e-01	1.78	1e-04
ENSG00000101439	CST3	-6.45	1e-30	-5.90	5e-24	3.19	2e-22	1.16	6e-02	-4.27	1e-08
ENSG00000100721	TCL1A	-6.46	2e-13	-7.16	5e-12	-2.40	3e-04	-4.88	1e-03	6.52	3e-41
ENSG00000163220	S100A9	-6.50	8e-32	-6.59	1e-27	1.21	3e-03	3.22	2e-14	-6.34	5e-14
ENSG00000132465	JCHAIN	-6.64	1e-07	-2.97	1e-02	-0.05	1e+00	-2.46	5e-01	3.90	6e-09
ENSG00000257764	AC020656.1	-6.64	1e-24	-5.11	2e-16	1.45	2e-04	2.93	5e-11	-4.59	1e-07
ENSG00000127951	FGL2	-6.68	9e-20	-5.79	2e-15	2.57	5e-13	1.83	5e-04	-4.03	8e-06
ENSG00000198502	HLA-DRB5	-6.70	1e-19	-3.27	3e-08	1.99	8e-08	-1.25	4e-01	1.76	3e-04
ENSG00000090382	LYZ	-6.81	8e-36	-7.11	3e-32	2.00	5e-09	2.45	5e-08	-7.44	4e-18
ENSG00000211592	IGKC	-6.90	2e-20	-7.77	3e-19	-4.33	1e-11	-5.49	2e-05	8.11	2e-70
ENSG00000121552	CSTA	-6.98	1e-24	-7.26	2e-21	1.99	1e-08	2.47	5e-08	-7.25	2e-11
ENSG00000172243	CLEC7A	-7.01	6e-17	-6.70	4e-14	2.37	2e-10	2.11	5e-05	-5.69	7e-07
ENSG00000197249	SERPINA1	-7.01	5e-21	-5.71	1e-15	2.66	1e-13	1.76	1e-03	-5.11	1e-07
ENSG00000211898	IGHD	-7.10	1e-13	-4.79	1e-08	-5.50	2e-11	-4.53	2e-03	8.48	3e-54
ENSG00000197629	MPEG1	-7.15	1e-17	-6.85	1e-14	1.81	3e-06	2.39	1e-06	-1.52	2e-01
ENSG00000085265	FCN1	-7.22	3e-28	-7.34	3e-24	2.26	3e-11	2.19	3e-06	-5.91	5e-11
ENSG00000196126	HLA-DRB1	-7.30	8e-32	-4.28	1e-15	1.78	4e-07	-0.63	9e-01	1.90	2e-05
ENSG00000211677	IGLC2	-7.40	2e-11	-7.10	3e-09	-6.80	2e-10	-6.83	2e-03	10.28	2e-48
ENSG00000100453	GZMB	-7.41	3e-11	3.25	9e-10	-1.16	3e-01	-4.24	3e-02	-0.14	1e+00
ENSG00000038427	VCAN	-7.48	1e-23	-6.59	1e-18	1.37	6e-04	3.09	2e-12	-7.16	2e-10
ENSG00000204287	HLA-DRA	-7.49	4e-38	-5.46	1e-23	1.82	1e-07	-0.23	1e+00	1.77	8e-05
ENSG00000203747	FCGR3A	-7.51	7e-14	0.11	1e+00	3.07	3e-11	-4.34	5e-03	-6.19	2e-05
ENSG00000163563	MNDA	-7.85	3e-25	-6.96	4e-20	1.58	5e-05	2.85	6e-10	-4.53	4e-07
ENSG00000163736	PPBP	-7.98	1e-03	-6.68	3e-02	-1.66	7e-01	6.10	5e-07	-5.67	9e-01

This plot shows the Sequencing Saturation metric as a function of downsampled sequencing depth in mean reads per cell, up to the observed sequencing depth. Sequencing Saturation is a measure of the observed library complexity, and approaches 1.0 (100%) when all converted mRNA transcripts have been sequenced. The slope of the curve near the endpoint can be interpreted as an upper bound to the benefit to be gained from increasing the sequencing depth beyond this point. The dotted line is drawn at a value reasonably approximating the saturation point.

Sequencing Saturation

This plot shows the Median Genes per Cell as a function of downsampled sequencing depth in mean reads per cell, up to the observed sequencing depth. The slope of the curve near the endpoint can be interpreted as an upper bound to the benefit to be gained from increasing the sequencing depth beyond this point.

Number of Reads	76,921,082
Valid Barcodes	96.6%
Sequencing Saturation	90.1%
Q30 Bases in Barcode	94.0%
Q30 Bases in RNA Read	88.3%
Q30 Bases in Sample Index	90.1%
Q30 Bases in UMI	92.8%

Reads Mapped to Genome	92.7%
Reads Mapped Confidently to Genome	90.1%
Reads Mapped Confidently to Intergenic Regions	3.6%
Reads Mapped Confidently to Intronic Regions	22.3%
Reads Mapped Confidently to Exonic Regions	64.1%
Reads Mapped Confidently to Transcriptome	60.8%
Reads Mapped Antisense to Gene	1.0%

Estimated Number of Cells	996
Fraction Reads in Cells	96.1%
Mean Reads per Cell	77,230
Median Genes per Cell	1,078
Total Genes Detected	16,063
Median UMI Counts per Cell	3,358

Name	pbmc_1k_v2
Description	Peripheral blood mononuclear cells (PBMCs) from a healthy donor
Transcriptome	GRCh38
Chemistry	Single Cell 3' v2
Cell Ranger Version	3.0.0

Estimated Number of Cells

Mean Reads per Cell

Median Genes per Cell

Sequencing

Mapping

Cells

Sample

Clustering Type:

t-SNE Projection of Cells Colored by UMI Counts

t-SNE projection of Cells Colored by Automated Clustering

Top Genes By Cluster (Log2 fold-change, p-value)

Sequencing Saturation

Median Genes per Cell