Brain tissue expression of CD44 in pons

PONS - Expression summary

Protein expressionⁱ

No data

RNA expressionⁱ

HPA Brain:	123.9	nTPM
FANTOM5:	414.3	Scaled Tags Per Million

Macaque:	27.8	nTPM
Mouse:	3.0	nTPM
Rat:	7.9	nTPM
Pig:	13.9	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+
Show allShow less

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
Show allShow less

This data was generated by Siletti K et al. (2023), re-processed by HPA (see methods) and simplified for global overview

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.	123.9

Sample id

Sample description

nTPM

Anterior cochlear nucleus, ventral
nTPM: 104.4

2301	Female, age 85, both hemispheres	158.1
2090	Male, age 80, both hemispheres	94.8
2188	Female, age 91, both hemispheres	85.5
1984	Male, age 76, both hemispheres	79.1

Dorsal cochlear nucleus
nTPM: 93.3

2187	Female, age 91, both hemispheres	120.7
2058	Male, age 76, both hemispheres	108.0
2370	Male, age 61, both hemispheres	104.1
2378	Male, age 80, both hemispheres	73.1
2802	Male, age 74, right hemisphere	60.8

Dorsal tegmental nucleus
nTPM: 123.9

2358	Male, age 61, both hemispheres	204.3
2326	Male, age 74, both hemispheres	99.9
1936	Male, age 76, left hemisphere	95.9
2083	Male, age 80, both hemispheres	95.3

Dorsolateral tegmental area
nTPM: 114.3

2337	Male, age 61, both hemispheres	201.6
2360	Male, age 74, both hemispheres	141.5
2654	Male, age 80, both hemispheres	90.2
2751	Female, age 85, both hemispheres	70.0
2141	Male, age 76, both hemispheres	68.1

Kolliker-Fuse nucleus
nTPM: 116.2

2315	Male, age 76, right hemisphere	230.1
2163	Male, age 80, both hemispheres	65.5
2793	Female, age 91, left hemisphere	53.0

Lateral lemniscal nuclei
nTPM: 48.1

2746	Female, age 85, left hemisphere	98.9
2169	Male, age 76, both hemispheres	44.6
2453	Male, age 74, right hemisphere	39.4
2036	Male, age 80, both hemispheres	34.0
2320	Female, age 91, left hemisphere	23.8

Lateral parabrachial nucleus
nTPM: 120.9

2792	Male, age 76, both hemispheres	150.9
2139	Female, age 85, right hemisphere	133.7
2013	Male, age 80, both hemispheres	101.9
2790	Male, age 61, both hemispheres	97.3

Lateral vestibular nucleus
nTPM: 82.2

2311	Male, age 80, both hemispheres	105.1
2184	Male, age 76, both hemispheres	59.4

Locus coeruleus
nTPM: 71.0

2123	Female, age 91, both hemispheres	104.2
2788	Male, age 74, unknown	84.0
2317	Female, age 72, unknown	78.6
1980	Male, age 76, both hemispheres	76.0
2014	Male, age 55, unknown	56.5
2162	Male, age 80, both hemispheres	53.2
2720	Male, age 74, both hemispheres	44.8

Medial parabrachial nucleus
nTPM: 91.5

2156	Male, age 61, both hemispheres	134.1
2170	Female, age 91, both hemispheres	115.4
2854	Male, age 80, both hemispheres	88.4
2786	Male, age 76, both hemispheres	63.9
2463	Female, age 85, right hemisphere	55.7

Medial periolivary nuclei
nTPM: 78.8

2791	Male, age 74, right hemisphere	166.2
2081	Male, age 80, both hemispheres	70.4
2063	Male, age 76, both hemispheres	57.1
2171	Female, age 85, both hemispheres	53.3
2458	Female, age 91, both hemispheres	46.8

Motor facial nucleus
nTPM: 74.8

2365	Male, age 74, right hemisphere	148.4
2126	Male, age 61, both hemispheres	94.6
2697	Female, age 85, both hemispheres	70.5
2795	Female, age 91, both hemispheres	56.8
2062	Male, age 76, both hemispheres	56.4
2327	Male, age 80, both hemispheres	22.2

Motor trigeminal nucleus
nTPM: 61.4

2335	Male, age 61, both hemispheres	101.7
2309	Male, age 76, both hemispheres	63.6
2321	Female, age 91, both hemispheres	51.5
2079	Male, age 80, both hemispheres	49.7
2560	Male, age 74, both hemispheres	40.4

Nuclei of the trapezoid body
nTPM: 58.2

1983	Male, age 76, both hemispheres	74.9
2159	Male, age 61, both hemispheres	61.4
2368	Female, age 91, both hemispheres	58.2
2735	Female, age 85, both hemispheres	51.3
2166	Male, age 80, both hemispheres	45.1

Nucleus raphe magnus
nTPM: 63.1

2455	Male, age 74, both hemispheres	105.2
2051	Male, age 76, both hemispheres	87.0
2172	Female, age 85, both hemispheres	60.6
2160	Male, age 61, both hemispheres	51.0
2328	Male, age 80, both hemispheres	40.0
2459	Female, age 91, both hemispheres	34.5

Paramedian reticular nucleus
nTPM: 96.4

2052	Male, age 76, both hemispheres	122.0
2313	Male, age 61, both hemispheres	98.6
2057	Male, age 80, both hemispheres	89.9
2050	Female, age 85, both hemispheres	75.0

Pedunculopontine tegmental nucleus
nTPM: 97.8

2338	Male, age 61, both hemispheres	156.8
2334	Male, age 80, both hemispheres	88.4
1921	Female, age 85, both hemispheres	48.2

Pontine nuclei
nTPM: 56.1

1863	Male, age 55, unknown	77.5
2109	Female, age 72, unknown	74.1
2115	Male, age 80, left hemisphere	67.1
2787	Female, age 85, both hemispheres	62.1
2319	Female, age 91, both hemispheres	51.1
1968	Male, age 76, left hemisphere	45.8
2727	Male, age 61, right hemisphere	43.8
2454	Male, age 74, left hemisphere	27.4

Pontine raphe nucleus
nTPM: 54.7

2853	Male, age 76, midline	57.1
2122	Female, age 85, midline	52.3

Posteroventral cochlear nucleus
nTPM: 75.4

2341	Male, age 80, both hemispheres	93.8
2135	Female, age 91, both hemispheres	85.3
2070	Male, age 76, both hemispheres	84.5
2371	Male, age 61, both hemispheres	68.2
2752	Female, age 85, both hemispheres	45.2

Principal sensory trigeminal nucleus
nTPM: 54.4

2324	Male, age 76, both hemispheres	86.8
2158	Male, age 61, both hemispheres	52.7
2008	Male, age 80, left hemisphere	39.3
2367	Female, age 91, left hemisphere	38.9

Reticular pontine nucleus, caudal
nTPM: 48.8

2092	Male, age 76, both hemispheres	82.5
2559	Male, age 74, both hemispheres	42.8
2457	Female, age 91, both hemispheres	42.4
2332	Male, age 80, right hemisphere	27.4

Reticular pontine nucleus, oral
nTPM: 59.4

1939	Male, age 80, both hemispheres	94.9
2012	Female, age 85, both hemispheres	66.9
2167	Male, age 76, both hemispheres	50.5
2361	Male, age 74, both hemispheres	45.7
2366	Female, age 91, both hemispheres	38.9

Reticulotegmental nucleus
nTPM: 56.4

2322	Female, age 91, both hemispheres	66.9
2333	Male, age 80, both hemispheres	60.8
2325	Male, age 76, both hemispheres	55.2
2452	Male, age 74, both hemispheres	42.8

Spinal trigeminal nucleus, oral
nTPM: 50.4

1978	Male, age 76, both hemispheres	61.3
2737	Female, age 85, both hemispheres	55.9
2164	Male, age 80, both hemispheres	34.0

Subcoeruleus area
nTPM: 57.5

1958	Male, age 80, both hemispheres	72.0
2369	Female, age 85, left hemisphere	71.7
2323	Female, age 91, left hemisphere	58.5
2089	Male, age 76, left hemisphere	47.3
2451	Male, age 74, both hemispheres	38.0

Superior olive
nTPM: 79.4

2364	Male, age 74, right hemisphere	185.4
1875	Female, age 85, both hemispheres	67.5
2020	Male, age 76, both hemispheres	66.3
2561	Female, age 91, both hemispheres	42.4
2329	Male, age 80, right hemisphere	35.7

Ventral periolivary nuclei
nTPM: 59.4

2130	Female, age 85, both hemispheres	83.5
2023	Male, age 76, both hemispheres	67.3
2165	Male, age 80, both hemispheres	50.5
2794	Female, age 91, left hemisphere	36.2

Ventrolateral tegmental area, A5 NE cell group
nTPM: 77.1

2840	Female, age 85, both hemispheres	118.1
2359	Male, age 61, both hemispheres	117.0
1959	Male, age 76, both hemispheres	75.1
2449	Male, age 74, both hemispheres	67.4
2161	Male, age 80, both hemispheres	46.7
2456	Female, age 91, both hemispheres	38.5

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.	414.3

FANTOM5 sample id

Sample description

Scaled Tags Per Million

Locus coeruleus
Scaled Tags Per Million: 414.3

FF:10182-103D2	60 years, female	430.5
FF:10165-103B3	76 years, female	398.1

Pons
Scaled Tags Per Million: 153.8

FF:10033-101E6

18-54 years, mixed

153.8

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.	27.8

Macaque sample

Sample description

nTPM

Pons
nTPM: 27.8

Samples: 2

Max nTPM: 30.6
Min nTPM: 24.9

Sample A		24.9
Sample B		30.6

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.	13.9

Pig sample

Sample description

nTPM

Pons
nTPM: 13.9

Samples: 3

Max nTPM: 15.4
Min nTPM: 11.7

Sample A	Female	11.7
Sample B	Female	14.5
Sample C	Male	15.4

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.	3.0

Mouse sample

Sample description

nTPM

Pons
nTPM: 3.0

Samples: 4

Max nTPM: 3.5
Min nTPM: 2.5

Sample A		2.5
Sample B		2.8
Sample C		3.2
Sample D		3.5

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.	7.9

Rat sample

Sample description

nTPM

Pons
nTPM: 7.9

Samples: 4

Max nTPM: 8.9
Min nTPM: 6.7

Sample A		8.9
Sample A		8.7
Sample A		7.4
Sample A		6.7