Brain tissue expression of SNCB in pons

PONS - Expression summary

Mouse brain, Intensity
Ponsⁱ

131.347

RNA expressionⁱ

HPA Brain:	389.9	nTPM
FANTOM5:	381.3	Scaled Tags Per Million

Macaque:	245.9	nTPM
Mouse:	393.7	nTPM
Rat:	583.1	nTPM
Pig:	366.7	nTPM

PONS - SINGLE NUCLEI RNA EXPRESSIONⁱ RNA expression in the single nuclei cluster types identified in this brain region visualized by a UMAP plot (top) and a bar chart (to the right). - UMAP PLOT visualizes the cells in each cluster; where each dot corresponds to a cell. For each individual cell, mouseover reveals read count and which cluster the cell belongs to. Hovering over a cluster name will highlight the corresponding cluster in the bar chart two the right. There are 2 options for color schemes: 1) cell type color, which is based on cell type groups used in the Single cell type part of the Single cell resource and 2) cluster color, which assigns a unique color to each cluster. There are 3 options for cell intensities: 1) Intensity, which color the individual cells according to % of max (log2(read_count+1)/log2(max(read_count)+1)100) in five different bins (<1%,<25%,<50%,<75%,≥75%) 2) Interval, which color the individual cells according to fixed interval of read count (0,1,2-4,5-9,>10) 3) Hexagon, which color the hexagon on average read count of all cells inside the hexagon - The BAR CHART* shows RNA expression (nTPM) in each cluster type. Hovering over the cluster name reveals nTPM value and number of included cells. Hovering over a bar highlights the corresponding cluster in the UMAP plot above. Color-coding can be toggled on the top of the page, between 2 options: 1) cell type color, which is based on cell type groups used in the Single cell type part of the Single cell resource and 2) cluster color, which assigns a unique color to each cluster.

SINGLE NUCLEI BRAIN - PONS, NEURONSⁱ

Cell type color

Cluster color

Colored according to cell type group

Read count filter: 0

Cluster		Cell type
	c-1	Excitatory (VGLUT1/2)
	c-2	Excitatory (VGLUT1) ETV1+ Z...
	c-3	Excitatory (VGLUT1/2)
	c-4	Excitatory (VGLUT1) ETV1+ Z...
	c-5	Excitatory (VGLUT1/2)
	c-6	Excitatory (VGLUT1/2)
	c-7	Excitatory (VGLUT1/2)
	c-8	Inhibitory (GAD1/2) SLC6A5+
	c-9	Excitatory (VGLUT2)
	c-10	Excitatory (VGLUT1/2)
	c-11	Excitatory (VGLUT1/2)
	c-12	Unassigned
	c-13	Inhibitory (GAD1/2) RORB+ K
	c-14	Inhibitory (GAD1/2) SST+
	c-15	Excitatory (VGLUT1) ETV1+ Z...
	c-16	Excitatory (VGLUT2)
	c-17	Excitatory (VGLUT1/2)
	c-18	Inhibitory (GAD1/2)
	c-19	Inhibitory (GAD1) PENK+ SST
	c-20	Excitatory (VGLUT2) FOXP2+
	c-21	Excitatory (VGLUT2) LMX1A+
	c-22	Excitatory (VGLUT2) MEIS2+
	c-23	Inhibitory (GAD1/2) SLC6A5+...
	c-24	Inhibitory (GAD1/2) SLC6A5+...
	c-25	Serotonergic SLC6A4+ SLC18A...
	c-26	Inhibitory (GAD1/2) PVALB+ ...
	c-27	Excitatory (VGLUT2)
	c-28	(VGLUT3) PENK+
	c-29	MEIS2+
	c-30	LMX1A+
	c-31	Inhibitory (GAD1/2) TAC1+
	c-32	Excitatory (VGLUT2) PVALB+
	c-33	Inhibitory (GAD1/2) PVALB+ ...
	c-34	Inhibitory (GAD1/2)
	c-35	Excitatory (VGLUT2) SST+ ME...
	c-36	LC Noradrenergic SLC6A2+ SL...
	c-37	Excitatory (VGLUT2) CRH+ FO...
	c-38	Inhibitory (GAD1/2) PVALB+ ...
	c-39	Excitatory (VGLUT2)
	c-40	Excitatory (VGLUT2) PVALB+
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This data was generated by Siletti K et al. (2023), re-processed by HPA (see methods) and simplified for global overview

SINGLE NUCLEI BRAIN - PONS, NON-NEURONALⁱ

Cell type color

Cluster color

Colored according to cell type group

Read count filter: 0

Cluster		Cell type
	c-1	Oligodendrocytes
	c-2	Oligodendrocytes
	c-3	Oligodendrocyte progenitor ...
	c-4	Oligodendrocytes
	c-5	Oligodendrocytes
	c-6	Oligodendrocytes
	c-7	Microglia
	c-8	Astrocytes
	c-9	Oligodendrocytes
	c-10	Astrocytes (CD44+)
	c-11	Oligodendrocytes
	c-12	Fibroblasts
	c-13	Vascular endothelial cells
	c-14	Pericytes
	c-15	Ependymal cells
	c-16	Lymphocytes
	c-17	Macrophages
	c-18	Microglia (SPP1+ HIF1A+)
	c-19	Bergmann glia
	c-20	Immature oligodendrocytes
	c-21	Oligodendrocyte progenitor ...
	c-22	Vascular smooth muscle cell
	c-23	Monocytes
	c-24	Immature oligodendrocytes
	c-25	Fibroblasts (BNC2+ KCNMA1+ ...
	c-26	Choroid plexus epithelial c...
	c-27	Macrophage Microglia double
	c-28	OPC & lymphocytes doublets
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This data was generated by Siletti K et al. (2023), re-processed by HPA (see methods) and simplified for global overview

PONS - Mouse brain profileⁱ Protein expression in mouse brain using immunofluorescence is reported as fluorescence intensity. , antibody HPA035876
Pons mean intensity	131.347
	intensityⁱ Protein expression in mouse brain using immunofluorescence is reported as mean fluorescence intensity.	FRONT BACK
Barrington's nucleus	-
Koelliker-fuse nucleus	-
Motor tregiminal nucleus	38.825
Parabrachial nucleus	44.905
Principle sensory trigeminal nucleus	60.359
Locus coeruleus	131.347
Pontine nucleus	67.227
Vestibular nucleus	12.455
Pontine reticular nucleus, oral	38.514
Lateral lemniscus	59.405
Superior paraolivary nucleus	18.746

PONS - HPA Brain Stereo-seq

PONS - HPA Brain RNA-seq

Max subtype nTPMⁱ Max subtype nTPM is the value for the subtype with the largest average nTPM across the subtype samples.	389.9

Sample id

Sample description

nTPM

Anterior cochlear nucleus, ventral
nTPM: 153.3

1984	Male, age 76, both hemispheres	186.1
2301	Female, age 85, both hemispheres	185.1
2188	Female, age 91, both hemispheres	138.7
2090	Male, age 80, both hemispheres	103.2

Dorsal cochlear nucleus
nTPM: 127.5

2370	Male, age 61, both hemispheres	146.1
2058	Male, age 76, both hemispheres	138.4
2187	Female, age 91, both hemispheres	136.6
2802	Male, age 74, right hemisphere	115.7
2378	Male, age 80, both hemispheres	100.9

Dorsal tegmental nucleus
nTPM: 142.8

2083	Male, age 80, both hemispheres	173.1
2358	Male, age 61, both hemispheres	164.4
1936	Male, age 76, left hemisphere	151.3
2326	Male, age 74, both hemispheres	82.2

Dorsolateral tegmental area
nTPM: 122.0

2141	Male, age 76, both hemispheres	187.5
2654	Male, age 80, both hemispheres	164.2
2751	Female, age 85, both hemispheres	120.8
2360	Male, age 74, both hemispheres	83.4
2337	Male, age 61, both hemispheres	54.0

Kolliker-Fuse nucleus
nTPM: 170.4

2793	Female, age 91, left hemisphere	231.8
2163	Male, age 80, both hemispheres	177.9
2315	Male, age 76, right hemisphere	101.5

Lateral lemniscal nuclei
nTPM: 306.7

2453	Male, age 74, right hemisphere	396.1
2169	Male, age 76, both hemispheres	364.2
2036	Male, age 80, both hemispheres	297.3
2746	Female, age 85, left hemisphere	267.3
2320	Female, age 91, left hemisphere	208.4

Lateral parabrachial nucleus
nTPM: 183.8

2139	Female, age 85, right hemisphere	311.8
2790	Male, age 61, both hemispheres	184.8
2013	Male, age 80, both hemispheres	174.6
2792	Male, age 76, both hemispheres	63.9

Lateral vestibular nucleus
nTPM: 156.4

2184	Male, age 76, both hemispheres	168.7
2311	Male, age 80, both hemispheres	144.1

Locus coeruleus
nTPM: 216.7

2720	Male, age 74, both hemispheres	329.1
2123	Female, age 91, both hemispheres	316.1
2162	Male, age 80, both hemispheres	210.4
1980	Male, age 76, both hemispheres	187.9
2014	Male, age 55, unknown	173.8
2317	Female, age 72, unknown	160.7
2788	Male, age 74, unknown	138.7

Medial parabrachial nucleus
nTPM: 178.7

2854	Male, age 80, both hemispheres	249.1
2156	Male, age 61, both hemispheres	206.2
2786	Male, age 76, both hemispheres	164.4
2170	Female, age 91, both hemispheres	147.1
2463	Female, age 85, right hemisphere	126.7

Medial periolivary nuclei
nTPM: 272.0

2171	Female, age 85, both hemispheres	486.9
2063	Male, age 76, both hemispheres	327.0
2791	Male, age 74, right hemisphere	227.1
2458	Female, age 91, both hemispheres	177.2
2081	Male, age 80, both hemispheres	142.1

Motor facial nucleus
nTPM: 296.0

2365	Male, age 74, right hemisphere	360.6
2327	Male, age 80, both hemispheres	358.6
2062	Male, age 76, both hemispheres	357.0
2697	Female, age 85, both hemispheres	330.0
2795	Female, age 91, both hemispheres	202.6
2126	Male, age 61, both hemispheres	167.3

Motor trigeminal nucleus
nTPM: 215.9

2079	Male, age 80, both hemispheres	286.8
2560	Male, age 74, both hemispheres	256.2
2335	Male, age 61, both hemispheres	216.0
2309	Male, age 76, both hemispheres	171.2
2321	Female, age 91, both hemispheres	149.2

Nuclei of the trapezoid body
nTPM: 333.9

2159	Male, age 61, both hemispheres	475.4
2735	Female, age 85, both hemispheres	412.0
1983	Male, age 76, both hemispheres	337.8
2166	Male, age 80, both hemispheres	251.9
2368	Female, age 91, both hemispheres	192.2

Nucleus raphe magnus
nTPM: 389.9

2172	Female, age 85, both hemispheres	545.1
2160	Male, age 61, both hemispheres	519.5
2455	Male, age 74, both hemispheres	479.6
2328	Male, age 80, both hemispheres	316.6
2051	Male, age 76, both hemispheres	277.3
2459	Female, age 91, both hemispheres	201.4

Paramedian reticular nucleus
nTPM: 216.9

2050	Female, age 85, both hemispheres	320.5
2313	Male, age 61, both hemispheres	254.1
2057	Male, age 80, both hemispheres	182.9
2052	Male, age 76, both hemispheres	109.9

Pedunculopontine tegmental nucleus
nTPM: 162.1

1921	Female, age 85, both hemispheres	187.1
2334	Male, age 80, both hemispheres	165.4
2338	Male, age 61, both hemispheres	133.7

Pontine nuclei
nTPM: 294.2

2787	Female, age 85, both hemispheres	535.7
1863	Male, age 55, unknown	353.9
2727	Male, age 61, right hemisphere	329.8
1968	Male, age 76, left hemisphere	328.4
2109	Female, age 72, unknown	253.9
2454	Male, age 74, left hemisphere	219.3
2115	Male, age 80, left hemisphere	194.6
2319	Female, age 91, both hemispheres	137.8

Pontine raphe nucleus
nTPM: 243.2

2122	Female, age 85, midline	287.3
2853	Male, age 76, midline	199.2

Posteroventral cochlear nucleus
nTPM: 117.8

2752	Female, age 85, both hemispheres	235.1
2070	Male, age 76, both hemispheres	158.7
2371	Male, age 61, both hemispheres	121.5
2341	Male, age 80, both hemispheres	61.3
2135	Female, age 91, both hemispheres	12.1

Principal sensory trigeminal nucleus
nTPM: 271.7

2158	Male, age 61, both hemispheres	438.3
2008	Male, age 80, left hemisphere	304.4
2367	Female, age 91, left hemisphere	183.7
2324	Male, age 76, both hemispheres	160.2

Reticular pontine nucleus, caudal
nTPM: 229.6

2332	Male, age 80, right hemisphere	370.1
2092	Male, age 76, both hemispheres	236.5
2457	Female, age 91, both hemispheres	181.0
2559	Male, age 74, both hemispheres	130.7

Reticular pontine nucleus, oral
nTPM: 199.6

2361	Male, age 74, both hemispheres	291.3
2012	Female, age 85, both hemispheres	226.0
2167	Male, age 76, both hemispheres	169.0
2366	Female, age 91, both hemispheres	168.7
1939	Male, age 80, both hemispheres	143.1

Reticulotegmental nucleus
nTPM: 205.2

2325	Male, age 76, both hemispheres	255.2
2333	Male, age 80, both hemispheres	197.6
2452	Male, age 74, both hemispheres	190.6
2322	Female, age 91, both hemispheres	177.6

Spinal trigeminal nucleus, oral
nTPM: 190.9

2737	Female, age 85, both hemispheres	200.7
1978	Male, age 76, both hemispheres	195.8
2164	Male, age 80, both hemispheres	176.4

Subcoeruleus area
nTPM: 198.0

2323	Female, age 91, left hemisphere	281.0
1958	Male, age 80, both hemispheres	251.2
2089	Male, age 76, left hemisphere	240.2
2451	Male, age 74, both hemispheres	129.7
2369	Female, age 85, left hemisphere	87.9

Superior olive
nTPM: 271.1

1875	Female, age 85, both hemispheres	362.6
2329	Male, age 80, right hemisphere	278.0
2561	Female, age 91, both hemispheres	257.5
2364	Male, age 74, right hemisphere	246.7
2020	Male, age 76, both hemispheres	210.7

Ventral periolivary nuclei
nTPM: 316.1

2130	Female, age 85, both hemispheres	408.7
2165	Male, age 80, both hemispheres	398.7
2794	Female, age 91, left hemisphere	281.8
2023	Male, age 76, both hemispheres	175.1

Ventrolateral tegmental area, A5 NE cell group
nTPM: 240.0

2449	Male, age 74, both hemispheres	400.6
2840	Female, age 85, both hemispheres	263.2
1959	Male, age 76, both hemispheres	262.4
2161	Male, age 80, both hemispheres	248.5
2359	Male, age 61, both hemispheres	139.4
2456	Female, age 91, both hemispheres	126.0

PONS - FANTOM5 CAGEⁱ

Max subtype Scaled Tags Per Millionⁱ Max subtype Scaled Tags Per Million is the value for the subtype with the largest average Scaled Tags Per Million across the subtype samples.	381.3

FANTOM5 sample id

Sample description

Scaled Tags Per Million

Locus coeruleus
Scaled Tags Per Million: 126.9

FF:10182-103D2	60 years, female	161.0
FF:10165-103B3	76 years, female	92.7

Pons
Scaled Tags Per Million: 381.3

FF:10033-101E6

18-54 years, mixed

381.3

PONS - Macaque RNA-seq

Max subtype nTPMⁱ Max subtype nTPM is the value for the subtype with the largest average nTPM across the subtype samples.	245.9

Macaque sample

Sample description

nTPM

Pons
nTPM: 245.9

Samples: 2

Max nTPM: 279.7
Min nTPM: 212.1

Sample A		279.7
Sample B		212.1

PONS - Pig RNA-seqⁱ

Max subtype nTPMⁱ Max subtype nTPM is the value for the subtype with the largest average nTPM across the subtype samples.	366.7

Pig sample

Sample description

nTPM

Pons
nTPM: 366.7

Samples: 3

Max nTPM: 644.1
Min nTPM: 220.9

Sample A	Female	644.1
Sample B	Female	220.9
Sample C	Male	235.2

PONS - Mouse RNA-seqⁱ

Max subtype nTPMⁱ Max subtype nTPM is the value for the subtype with the largest average nTPM across the subtype samples.	393.7

Mouse sample

Sample description

nTPM

Pons
nTPM: 393.7

Samples: 4

Max nTPM: 406.2
Min nTPM: 384.6

Sample A		387.4
Sample B		396.7
Sample C		406.2
Sample D		384.6

PONS - Rat RNA-seq

Max subtype nTPMⁱ Max subtype nTPM is the value for the subtype with the largest average nTPM across the subtype samples.	583.1

Rat sample

Sample description

nTPM

Pons
nTPM: 583.1

Samples: 4

Max nTPM: 626.3
Min nTPM: 518.5

Sample A		626.3
Sample A		599.4
Sample A		518.5
Sample A		588.0