SMI Data File ReadMe v1

Transcript File

Lung5_Rep2_tx_file.csv : 3.7 GB

fov	cell_ID	x_global_px	y_global_px	x_local_px	y_local_px	z	target	CellComp
1	135	12059.69	162613.4	4709.695	3441.217	2	HLA-A	Cytoplasm
1	135	12065.03	162624.8	4715.033	3452.533	2	MXRA8	Cytoplasm
1	135	12065.57	162626.4	4715.575	3454.138	2	MT1X	Cytoplasm
1	135	12057.36	162633.1	4707.362	3460.925	2	FZD6	Cytoplasm
1	135	12055.38	162632.0	4705.375	3459.750	2	IGFBP7	Cytoplasm
1	135	12056.98	162610.1	4706.980	3437.860	2	RPL22	Cytoplasm
1	135	12066.88	162623.7	4716.880	3451.440	2	KRT13	Cytoplasm
1	135	12063.75	162613.6	4713.750	3441.375	2	IGKC	Cytoplasm
1	135	12056.57	162630.4	4706.574	3458.179	2	GPX3	Cytoplasm
1	135	12059.90	162632.5	4709.900	3460.275	2	LGALS3BP	Cytoplasm

• Column descriptions:
  • fov
    • The Field Of View (FOV) the transcript is in. All FOVs from the sample are contained within this transcript file.
  • cell_ID
    • Unique identifier for a single cell within a given FOV. To make a unique identifier for a cell within the whole sample use both the “fov” and “cell_ID” columns. Transcripts not assigned to cells have a value of 0.
  • x_global_px
    • See “x_local_px” description. The global positions describes the relative position of this transcript within the large sample reference frame.
  • y_global_px
    • Same as “x_global_px” but for the y dimension
  • x_local_px
    • The x position of this transcipt within the FOV, measured in pixels. To convert to microns multiply the pixel value by 0.18 um per pixel.
  • y_local_px
    • Same as “x_local_px” but for the y dimension
  • z
    • The Z-slice image number. This has an arbitrary unit.
  • target
    • The gene detected. HUGO gene symbols are used.
  • CellComp +The subcellular compartment (Nuclear, Membrane, or Cytoplasmic. “0” denotes Extracellular) in which the transcript was detected as determined by cell segmentation algorithm.

Cell Expression File

Lung5_Rep2_exprMat_file.csv : 210.4 MB

	fov	cell_ID	AATK	ABL1	ABL2	ACE	ACE2	ACKR1	ACKR3	ACKR4	ACTA2	ACTG2	ACVR1	ACVR1B	ACVR2A	ACVRL1	ADGRA2	ADGRA3	ADGRB2	ADGRB3	ADGRD1	ADGRE1	ADGRE2	ADGRE5	ADGRF1	ADGRF3	ADGRF4	ADGRF5	ADGRG1	ADGRG2	ADGRG3	ADGRG5	ADGRG6	ADGRL1	ADGRL2	ADGRL4	ADGRV1	ADIPOQ	ADIRF	ADM2	ADORA2A	AGR2	AHI1	AHR	AKT1	ALCAM	ANGPT1	ANGPT2	ANGPT4	ANGPTL1	ANXA1	ANXA2	ANXA4	APOA1	APOB	APOD	APP	AQP3	AR	AREG	ARF1	ARG1	ARHGDIB	ARTN	ATF3	ATG10	ATG12	ATG5	ATM	ATR	AXL	AZGP1	AZU1	B2M	B3GNT7	BAG3	BATF3	BAX	BCL2	BCL2L1	BECN1	BEST1	BGN	BID	BIRC5	BMP1	BMP2	BMP3	BMP4	BMP5	BMP6	BMP7	BMPR1A	BMPR2	BMX	BRCA1	BST1	BST2	BTG1	BTK	C11orf96	C1QA	C1QB	C1QC	C5AR2	C9orf16	CALB1	CALD1	CALM1	CALM2	CALM3	CAMP	CASP3	CASP8	CASR	CAV1	CCL11	CCL13	CCL15	CCL18	CCL19	CCL2	CCL20	CCL21	CCL23	CCL26	CCL28	CCL3	CCL3L3	CCL4	CCL4L2	CCL5	CCL7	CCL8	CCND1	CCR1	CCR10	CCR2	CCR5	CCR7	CCRL2	CD14	CD163	CD164	CD19	CD2	CD209	CD24	CD27	CD274	CD276	CD28	CD300A	CD33	CD34	CD36	CD37	CD38	CD3D	CD3E	CD3G	CD4	CD40	CD40LG	CD44	CD47	CD48	CD52	CD53	CD55	CD58	CD59	CD5L	CD63	CD68	CD69	CD70	CD74	CD79A	CD80	CD81	CD83	CD84	CD86	CD8A	CD8B	CD9	CDH1	CDH11	CDH5	CDKN1A	CDKN3	CEACAM1	CEACAM6	CELSR1	CELSR2	CENPF	CFD	CFLAR	CHEK1	CHEK2	CHGA	CHI3L1	CIDEA	CIITA	CLCF1	CLDN4	CLEC10A	CLEC12A	CLEC14A	CLEC1A	CLEC2B	CLEC2D	CLEC4A	CLEC4D	CLEC4E	CLEC5A	CLEC7A	CLOCK	CLU	CMKLR1	CNTFR	COL11A1	COL12A1	COL14A1	COL15A1	COL16A1	COL17A1	COL18A1	COL1A1	COL1A2	COL21A1	COL27A1	COL3A1	COL4A1	COL4A2	COL4A5	COL5A1	COL5A2	COL5A3	COL6A1	COL6A2	COL6A3	COL8A1	COL9A1	COL9A2	COL9A3	COTL1	CPA3	CPB1	CRIP1	CRP	CRYAB	CSF1	CSF1R	CSF2	CSF2RA	CSF2RB	CSF3	CSF3R	CSHL1	CSK	CST7	CTLA4	CTNNB1	CTSG	CTSW	CUZD1	CX3CL1	CX3CR1	CXCL1	CXCL10	CXCL12	CXCL14	CXCL16	CXCL17	CXCL2	CXCL3	CXCL5	CXCL6	CXCL8	CXCL9	CXCR1	CXCR2	CXCR3	CXCR4	CXCR5	CXCR6	CYP19A1	CYP1B1	CYSTM1	CYTOR	DCN	DDC	DDIT3	DDR1	DDR2	DDX58	DHRS2	DLL1	DMBT1	DNMT1	DNMT3A	DNTT	DPP4	DST	DUSP1	DUSP2	DUSP4	DUSP5	DUSP6	EFNA1	EFNA4	EFNA5	EFNB1	EFNB2	EFNB3	EGF	EGFR	EIF5A	ELANE	EMP3	ENG	ENTPD1	EOMES	EPCAM	EPHA2	EPHA3	EPHA4	EPHA7	EPHB2	EPHB3	EPHB4	EPHB6	EPOR	ERBB2	ERBB3	ESAM	ESR1	ETS1	ETV4	ETV5	EZH2	EZR	FABP4	FABP5	FAS	FASLG	FASN	FCER1G	FCGBP	FCGR3A	FCRLA	FES	FFAR2	FFAR3	FFAR4	FGF1	FGF12	FGF13	FGF18	FGF2	FGF7	FGF9	FGFR1	FGFR2	FGFR3	FGG	FGR	FKBP11	FLT1	FLT3LG	FN1	FOS	FOXF1	FOXP3	FPR1	FYB1	FYN	FZD1	FZD3	FZD4	FZD5	FZD6	FZD7	FZD8	G6PC2	G6PD	GADD45B	GAS6	GATA3	GC	GCG	GDF10	GDF15	GDF3	GDF6	GDF9	GDNF	GLUD1	GLUL	GNLY	GPBAR1	GPER1	GPNMB	GPR183	GPX1	GPX3	GSN	GSTP1	GZMA	GZMB	GZMH	GZMK	H2AZ1	H4C3	HAVCR2	HBA1	HBB	HCAR2	HCAR3	HCK	HCST	HDAC1	HDAC11	HDAC3	HDAC4	HDAC5	HGF	HIF1A	HILPDA	HLA.A	HLA.B	HLA.C	HLA.DPA1	HLA.DPB1	HLA.DQA1	HLA.DQB1	HLA.DRA	HLA.DRB1	HLA.DRB5	HLA.E	HMGB2	HMGN2	HPGDS	HSD17B2	HSD3B2	HSP90AA1	HSP90AB1	HSP90B1	HSPA1A	HSPA1B	HSPB1	HTT	IAPP	ICAM1	ICAM2	ICAM3	ICOS	ICOSLG	IDO1	IER3	IFI27	IFIH1	IFIT1	IFITM1	IFITM3	IFNA1	IFNAR1	IFNAR2	IFNB1	IFNG	IFNGR1	IFNGR2	IFNL2	IFNL3	IGF1	IGF1R	IGF2	IGF2R	IGFBP3	IGFBP5	IGFBP6	IGFBP7	IGHA1	IGHD	IGHG1	IGHG2	IGHM	IGKC	IL10	IL10RA	IL10RB	IL11	IL11RA	IL12A	IL12B	IL12RB1	IL12RB2	IL13RA1	IL15	IL15RA	IL16	IL17A	IL17B	IL17D	IL17RA	IL17RB	IL17RE	IL18	IL18R1	IL1A	IL1B	IL1R1	IL1R2	IL1RAP	IL1RL1	IL1RN	IL2	IL20	IL20RA	IL22RA1	IL23A	IL24	IL27RA	IL2RA	IL2RB	IL2RG	IL32	IL33	IL34	IL36G	IL3RA	IL4R	IL6	IL6R	IL6ST	IL7	IL7R	INHA	INHBA	INHBB	INS	INSR	IRF3	IRF4	ITGA1	ITGA2	ITGA3	ITGA5	ITGA6	ITGA9	ITGAE	ITGAL	ITGAM	ITGAV	ITGAX	ITGB1	ITGB2	ITGB4	ITGB5	ITGB6	ITGB8	ITK	ITM2A	JAG1	JAK1	JAK2	JCHAIN	JUN	JUNB	KDR	KIT	KITLG	KLF2	KLK3	KLRB1	KLRK1	KRAS	KRT1	KRT10	KRT13	KRT14	KRT15	KRT16	KRT17	KRT18	KRT19	KRT20	KRT23	KRT24	KRT4	KRT5	KRT6A	KRT6B	KRT6C	KRT7	KRT8	KRT80	KRT86	LAG3	LAIR1	LAMP2	LAMP3	LCN2	LDLR	LEFTY1	LEFTY2	LEP	LGALS1	LGALS3	LGALS3BP	LGALS9	LIF	LIFR	LINC02446	LMNA	LPAR5	LTB	LTBR	LTF	LUM	LY6D	LY75	LYN	LYZ	MAF	MALAT1	MAML2	MAP1LC3B	MAPK13	MAPK14	MARCO	MECOM	MEG3	MERTK	MET	MGP	MIF	MKI67	MMP1	MMP10	MMP12	MMP14	MMP16	MMP19	MMP2	MMP3	MMP7	MMP8	MMP9	MPO	MRC1	MRC2	MS4A1	MS4A4A	MSMB	MST1R	MT1X	MT2A	MTOR	MTRNR2L1	MX1	MXRA8	MYC	MYH11	MYL9	MZB1	MZT2A	NANOG	NCR1	NDRG1	NEAT1	NFKB1	NFKBIA	NGFR	NKG7	NLRC4	NLRC5	NLRP1	NLRP2	NLRP3	NOD2	NOSIP	NOTCH1	NOTCH2	NOTCH3	NPPB	NPPC	NPR1	NPR2	NPR3	NR1H2	NR1H3	NR1H4	NR3C1	NRG1	NRG4	NRIP3	NRXN1	NRXN3	NTRK2	OAS1	OAS2	OAS3	OASL	OLFM4	OLR1	OSM	OSMR	OXER1	OXGR1	P2RX5	P2RY12	PARP1	PCNA	PDCD1	PDCD1LG2	PDGFA	PDGFB	PDGFC	PDGFD	PDGFRA	PDGFRB	PECAM1	PF4	PGF	PGR	PHLDA2	PIGR	PLA2R1	PLAC8	PNOC	POU5F1	PPARA	PPARD	PPARG	PPBP	PRF1	PROK2	PROKR1	PRSS2	PSAP	PSCA	PTGDR2	PTGDS	PTGES	PTGES2	PTGES3	PTGIS	PTGS1	PTGS2	PTHLH	PTK2	PTK6	PTPRC	PTPRCAP	PTTG1	QRFPR	RAC1	RAC2	RAD51	RAMP1	RAMP2	RAMP3	RARA	RARB	RARG	RARRES1	RARRES2	RB1	RBPJ	REG1A	RELA	RELT	RGCC	RGS1	RGS2	RGS5	RNF43	ROR1	RORA	RPL21	RPL22	RPL32	RPL34	RPL37	RPS4Y1	RSPO1	RSPO2	RSPO3	RUNX3	RXRA	RXRB	RYK	S100A10	S100A2	S100A4	S100A6	S100A8	S100A9	S100B	S100P	SAA1	SAA2	SAT1	SCG5	SCGB3A1	SEC23A	SEC61G	SELENOP	SELL	SELPLG	SERPINA1	SERPINA3	SERPINB5	SERPINH1	SFN	SIGIRR	SLC2A1	SLC2A4	SLC40A1	SLPI	SMAD2	SMAD3	SMAD4	SMARCB1	SMO	SNAI1	SNAI2	SOD1	SOD2	SOSTDC1	SOX2	SOX4	SOX9	SPARCL1	SPINK1	SPOCK2	SPP1	SPRY2	SPRY4	SQSTM1	SRC	SREBF1	SRGN	SST	ST6GAL1	ST6GALNAC3	STAT1	STAT3	STAT4	STAT5A	STAT5B	STAT6	STMN1	SUCNR1	SYK	TACSTD2	TAGLN	TAP1	TAP2	TBX21	TCL1A	TEK	TFEB	TGFB1	TGFB2	TGFB3	TGFBR1	TGFBR2	THBS1	THBS2	TIE1	TIGIT	TIMP1	TLR1	TLR2	TLR3	TLR4	TLR5	TLR7	TLR8	TM4SF1	TNF	TNFAIP6	TNFRSF10A	TNFRSF10B	TNFRSF10D	TNFRSF11A	TNFRSF11B	TNFRSF12A	TNFRSF13B	TNFRSF14	TNFRSF17	TNFRSF18	TNFRSF19	TNFRSF1A	TNFRSF1B	TNFRSF21	TNFRSF4	TNFRSF9	TNFSF10	TNFSF12	TNFSF13B	TNFSF14	TNFSF15	TNFSF18	TNFSF4	TNFSF8	TNFSF9	TOP2A	TOX	TP53	TPM1	TPM2	TPSAB1	TPSB2	TSC22D1	TSHZ2	TSLP	TTR	TUBB	TUBB4B	TWIST1	TWIST2	TXK	TYK2	TYMS	TYROBP	UBE2C	UCP1	UPK3A	VCAM1	VCAN	VEGFA	VEGFB	VEGFC	VEGFD	VHL	VIM	VPREB3	VSIR	VTN	VWF	WIF1	WNT10B	WNT11	WNT2	WNT2B	WNT3	WNT5A	WNT5B	WNT7A	WNT7B	WNT9A	XBP1	XCL1	XCL2	YBX3	YES1	ZFP36	NegPrb3	NegPrb5	NegPrb6	NegPrb7	NegPrb8	NegPrb9	NegPrb10	NegPrb11	NegPrb12	NegPrb13	NegPrb14	NegPrb15	NegPrb16	NegPrb17	NegPrb18	NegPrb19	NegPrb20	NegPrb21	NegPrb22	NegPrb23
2	1	998	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	1	1	0	0	0	1	0	0	27	0	0	0	0	0	1	1	0	0	4	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	4	0	16	5	29	2	0	1	0	1	2	1	0	0	0	0	1	0	2	0	4	0	0	0	0	0	0	0	2	0	1	0	0	0	0	0	0	0	0	0	0	0	0	30	2	0	0	4	0	0	0	0	0	1	0	0	0	2	1	0	0	0	0	1	0	0	0	0	0	5	0	0	0	0	13	13	0	0	3	0	0	6	0	1	0	0	0	1	1	0	0	0	1	1	0	0	0	0	1	0	0	0	0	0	0	0	1	0	1	0	1	2	1	2	0	0	0	0	2	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	17	0	4	0	0	0	1	0	0	0	0	2	0	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	3	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	13	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	5	0	24	1	3	0	0	1	0	1	0	0	2	0	0	0	1	0	1	0	1	0	0	0	1	0	1	0	0	0	1	0	0	1	0	1	0	1	1	2	0	0	0	0	0	0	0	2	0	0	1	12	2	0	0	4	0	6	6	1	1	2	0	0	0	1	1	1	1	0	0	0	1	1	1	0	0	0	0	0	5	0	38	7	4	6	4	1	4	20	7	2	3	0	0	0	0	0	1	3	4	0	7	0	0	0	1	0	1	1	0	0	2	0	1	0	1	3	0	0	0	1	0	0	1	0	1	1	0	0	0	0	0	0	0	1	0	1	1	1	1	0	4	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	2	1	0	0	0	0	0	0	0	2	1	0	1	0	0	0	1	0	2	3	1	0	0	0	1	0	0	2	0	0	1	1	1	9	0	0	0	0	0	1	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	2	0	0	0	0	0	0	2	1	0	0	0	0	1	0	2	2	0	0	1	0	0	2	4	7	0	1	0	0	0	0	0	0	5	0	0	1	0	0	4	2	7	0	0	1	1	0	1	0	0	0	0	4	1	0	0	0	1	0	0	0	0	1	0	2	0	2	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	30	0	0	0	25	0	0	0	0	0	0	1	0	0	1	2	0	0	0	0	4	0	0	0	0	0	1	0	0	0	0	0	0	0	0	2	0	0	1	0	4	0	0	0	0	0	0	0	0	1	2	2	2	0	0	1	4	0	0	0	0	0	0	1	1	0	0	1	1	0	0	0	0	0	13	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	1	1	0	0	1	1	0	2	0	0	1	0	4	2	0	0	0	0	4	2	0	1	0	0	0	0	0	2	1	0	0	0	0	0	0	0	1	0	0	1	1	22	0	0	1	0	4	0	0	1	0	0	0	0	0	0	0	7	0	0	0	0	0	0	0	0	0	7	0	0	0	0	0	0	1	1	0	0	0	1	2	8	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	3	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	5	0	1	1	2	0	0	1	0	0	0	2	0	3	0	0	2	0	0	1	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	18	1	0	0	0	0	0	0	0	0	0	0	1	6	1	0	0	0	2	0	0	0	0	0	0	1	2	2	0	1	0	0	4	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
3	1	999	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	8	0	0	2	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	2	0	0	0	0	1	0	1	0	0	1	0	2	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	2	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	2	2	1	0	0	0	0	0	0	0	0	0	5	0	2	1	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	3	0	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	3	0	0	0	1	0	0	1	0	0	1	0	1	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	4	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	2	1	0	0	1	0	1	0	0	1	0	0	0	0	1	0	0	0	1	0	3	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	1	2	6	0	0	1	2	0	0	0	0	2	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	1	0	0	0	0	1	0	0	0	1	2	0	0	0	2	0	0	0	0	0	0	0	0	2	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	4	0	0	0	0	1	2	0	0	12	1	0	1	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	0	1	0	0	0	0	0	0	2	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	11	0	0	0	0	0	0	5	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	2	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	2	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	4	0	1	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	9	0	0	0	0	1	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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11	1	1007	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	0	0	2	0	0	0	0	0	1	2	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	2	0	0	0	0	0	0	0	1	0	0	4	0	0	0	0	0	0	1	0	2	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	1	2	0	0	0	0	0	0	0	2	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	2	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	13	1	2	0	3	0	2	0	0	0	0	0	1	1	0	0	8	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	1	0	0	0	0	0	1	0	0	3	0	0	1	0	0	1	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	1	1	0	1	7	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	9	2	1	1	0	0	0	0	1	2	0	0	0	0	0	0	0	0	5	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	6	0	0	0	0	0	5	0	1	0	1	0	0	0	0	0	3	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	1	0	0	0	0	0	4	0	0	1	3	2	0	1	0	0	1	0	0	0	0	2	2	2	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	10	0	0	0	0	0	1	1	0	0	1	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	2	0	0	0	0	0	0	0	0	22	1	0	2	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	7	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	4	0	2	0	0	0	0	0	1	0	0	0	1	1	0	2	1	2	1	0	0	1	0	0	1	0	0	0	0	0	2	0	1	3	0	0	0	5	5	0	1	7	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	0	2	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	1	0	0	1	1	0	0	0	1	1	0	0	0	1	0	1	0	1	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	4	0	0	0	0	22	0	0	0	0	1	0	1	1	1	0	0	0	4	0	0	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

• Column descriptions:
  • fov
    • The Field Of View (FOV) the transcript is in. All FOVs from the sample are contained within this Cell Expression file.
  • cell_ID
    • Unique identifier for a single cell within a given FOV. To make a unique identifier for a cell within the whole sample use both the “fov” and “cell_ID” columns. All transcripts not assigned to a cell are show with a “cell_ID” value of 0.
  • Gene expression target (AATK, ABL1, …, etc)
    • The number of transcripts observed for a given gene target for a given cell.
  • Negative probes (i.e. NegPrb##)
    • Negative probes, which do not match any sequence within the transcriptome or genome, are included. These can be used to assess background levels.

Cell Metadata File

Lung5_Rep2_metadata_file.csv : 12.0 MB

fov	cell_ID	Area	AspectRatio	CenterX_local_px	CenterY_local_px	CenterX_global_px	CenterY_global_px	Width	Height	Mean.MembraneStain	Max.MembraneStain	Mean.PanCK	Max.PanCK	Mean.CD45	Max.CD45	Mean.CD3	Max.CD3	Mean.DAPI	Max.DAPI
1	1	2142	1.48	806	3628	8156	162800.2	59	40	1075	1842	22954	49711	76	385	0	78	1784	11384
1	2	2236	2.08	980	3630	8330	162802.2	75	36	1232	4073	23035	65311	90	10963	0	248	2751	17658
1	3	4845	1.15	1637	3607	8987	162779.2	94	82	4367	11890	1593	26734	225	1329	5	283	8988	35448
1	4	2915	1.00	1694	3619	9044	162791.2	59	59	6017	13814	12387	50409	54	623	0	96	69	3837
1	5	8634	1.02	1869	3596	9219	162768.2	106	104	3945	13832	10624	47795	42	10543	0	85	227	6058
1	6	2248	0.66	2208	3617	9558	162789.2	41	62	1918	5078	7462	25661	31	268	0	0	1983	11738
1	7	5147	1.09	2270	3610	9620	162782.2	84	77	3210	10551	715	11854	20	264	0	16	5498	29958
1	8	3798	2.17	2561	3622	9911	162794.2	115	53	2732	8958	6951	43479	813	45043	0	148	2218	21364
1	9	3790	3.16	2665	3630	10015	162802.2	117	37	5468	13925	849	6014	358	7788	7	386	8381	35995
1	10	3901	1.35	3402	3620	10752	162792.2	77	57	4676	10663	270	666	34	501	0	100	12053	36001

• Column descriptions:
  • fov
    • The Field Of View (FOV) the transcript is in. All FOVs from the sample are contained within this Cell Metadata file.
  • cell_ID
    • Unique identifier for a single cell within a given FOV. To make a unique identifier for a cell within the whole sample use both the “fov” and “cell_ID” columns.
  • Area
    • Number of pixels assigned to a given cell.
  • Aspect Ratio
    • width divided by height.
  • CenterX_global_px
    • See “CenterX_local_px” description. The global positions describes the relative position of this transcript within the large sample reference frame.
  • CenterY_global_px
    • Same as “CenterX_global_px” but for the y dimension
  • CenterX_local_px
    • The x position of this transcipt within the FOV, measured in pixels. The pixel edge length is 180nm. Thus, to convert to microns multiply the pixel value by 0.18 um per pixel.
  • CenterY_local_px
    • Same as “CenterX_local_px” but for the y dimension
  • Width
    • Cell’s maximum length in x dimension (pixels)
  • Height
    • Cell’s maximum length in y dimension (pixels)
  • Mean.MembraneStain
    • Mean fluorescence intensity within a given cell for the channel detecting the membrane stain.
  • Max.MembraneStain
    • Maximum fluorescence intensity within a given cell for the channel detecting the membrane stain.
  • Mean.PanCK
    • Mean fluorescence intensity within a given cell for the Green Channel.
    • As the morphology markers are customizable this column will change to match the requested markers in each experiment.
  • Max.PanCK
    • Maximum fluorescence intensity within a given cell for the Green Channel.
    • As the morphology markers are customizable this column will change to match the requested markers in each experiment.
  • Mean.CD45
    • Mean fluorescence intensity within a given cell for the Yellow Channel.
    • As the morphology markers are customizable this column will change to match the requested markers in each experiment.
  • Max.CD45
    • Maximum fluorescence intensity within a given cell for the Yellow Channel.
    • As the morphology markers are customizable this column will change to match the requested markers in each experiment.
  • Mean.CD3
    • Mean fluorescence intensity within a given cell for the Red Channel.
    • As the morphology markers are customizable this column will change to match the requested markers in each experiment.
  • Max.CD3
    • Maximum fluorescence intensity within a given cell for the Red Channel.
    • As the morphology markers are customizable this column will change to match the requested markers in each experiment.
  • Mean.DAPI
    • Mean fluorescence intensity within a given cell for the DAPI Channel.
  • Max.DAPI
    • Maximum fluorescence intensity within a given cell for the DAPI Channel.

FOV Positions File

This file is used to reference each FOV within the global structure of the sample.

Lung5_Rep2_fov_positions_file.csv : 1.1 kB

fov	x_global_px	y_global_px
1	7350.00	159172.2
2	12822.22	159172.2
3	18294.44	159172.2
4	23766.67	159172.2
5	29238.89	159172.2
6	7350.00	162822.2
7	12822.22	162822.2
8	18294.44	162822.2
9	23766.67	162822.2
10	29238.89	162822.2

• Column descriptions:
  • fov
    • The Field Of View (FOV) number.
  • x_global_px
    • The relative x position of this the FOV, measured in pixels. To convert to microns multiply the pixel value by 0.18 um per pixel. All FOVs are the same dimension, 5472 x 3648 pixels.
  • y_global_px
    • See “x_global_px” description, but in for the y dimension.

CellComposite Images

Each FOV has a CellComposite image that displays the ImmunoFluorescence intesity from the IHC markers selected for the SMI experiment.

• Channels
  • Green
    • PanCK
  • Red
    • CD45
  • Grey
    • CD3
  • Blue
    • DAPI

CellOverlay Images

Each FOV has a CellOverlay image that displays the cell boundries determined during cell segmentation, shown as cyan lines.

CellLabels Images

Each FOV has a CellLabels image that displays the cell definitions determined during cell segmentation. Each cell identified is given a unique number (cell_ID) and all pixels determined to be within that cell have an intensity value matching that number. These cell_ID values are shared in the transcript, Cell Expression, and Cell Metadata files. A pixel not assigned to a cell has a “0” value.

CompartmentLabels Images

Each FOV has a CompartmentLabels image that displays the subcellular compartment definitions determined during cell segmentation. Each compartment type is given a unique number and all pixels determined to be within that compartment type have an intensity value matching that number.

• Compartment types
  0. Extracellular
  1. Nuclear
  2. Membrane
  3. Cytoplasmic

Raw Morphology Images

The raw TIF image files for each FOV (i.e. “FOV###” in file name). All Z-stacks are included (i.e. “Z###” in file name). These are used for cell segmentation and to produce the cellComposite jPEG images. Each image is ~195Mb, 8 images per FOV.

• Channels
  1. Membrane stain
  2. PanCK
  3. CD45
  4. CD3
  5. DAPI

Processed Giotto object (All Slides)

For ease of sharing and analysis the data from all slides has been loaded into a single Giotto object, from the Giotto toolbox for integrative analysis of spatial expression data. The Giotto package can be found here (https://github.com/RubD/Giotto). To use this object please use the “suite” branch of the Giotto package, specifically commit 0c8c2866e881b1c6b35ddc97c24dcb58b555c375 which was used for this analysis.

• Giotto publication
  • Dries, R., Zhu, Q. et al. Giotto: a toolbox for integrative analysis and visualization of spatial expression data. Genome Biol. 2021 Mar 8;22(1):78.
  • https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02286-2