Brain tissue expression of NEFM in pons

PONS - Expression summary

Protein expressionⁱ

No data

RNA expressionⁱ

HPA Brain:	1159.7	nTPM
FANTOM5:	2197.6	Scaled Tags Per Million

Rat:	304.2	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 - 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.	1159.7

Sample id

Sample description

nTPM

Anterior cochlear nucleus, ventral
nTPM: 387.0

1984	Male, age 76, both hemispheres	577.9
2301	Female, age 85, both hemispheres	477.9
2188	Female, age 91, both hemispheres	331.0
2090	Male, age 80, both hemispheres	161.2

Dorsal cochlear nucleus
nTPM: 339.9

2187	Female, age 91, both hemispheres	382.7
2802	Male, age 74, right hemisphere	362.1
2370	Male, age 61, both hemispheres	358.7
2378	Male, age 80, both hemispheres	332.4
2058	Male, age 76, both hemispheres	263.6

Dorsal tegmental nucleus
nTPM: 313.0

2083	Male, age 80, both hemispheres	402.2
2358	Male, age 61, both hemispheres	338.0
1936	Male, age 76, left hemisphere	327.7
2326	Male, age 74, both hemispheres	184.3

Dorsolateral tegmental area
nTPM: 180.8

2654	Male, age 80, both hemispheres	267.6
2751	Female, age 85, both hemispheres	212.7
2141	Male, age 76, both hemispheres	182.5
2360	Male, age 74, both hemispheres	174.2
2337	Male, age 61, both hemispheres	67.1

Kolliker-Fuse nucleus
nTPM: 781.1

2163	Male, age 80, both hemispheres	1663.6
2793	Female, age 91, left hemisphere	524.6
2315	Male, age 76, right hemisphere	155.0

Lateral lemniscal nuclei
nTPM: 646.8

2453	Male, age 74, right hemisphere	1087.2
2169	Male, age 76, both hemispheres	904.6
2320	Female, age 91, left hemisphere	600.9
2746	Female, age 85, left hemisphere	362.0
2036	Male, age 80, both hemispheres	279.2

Lateral parabrachial nucleus
nTPM: 343.0

2139	Female, age 85, right hemisphere	557.4
2790	Male, age 61, both hemispheres	396.2
2013	Male, age 80, both hemispheres	274.4
2792	Male, age 76, both hemispheres	144.2

Lateral vestibular nucleus
nTPM: 1159.7

2184	Male, age 76, both hemispheres	1958.9
2311	Male, age 80, both hemispheres	360.5

Locus coeruleus
nTPM: 499.3

2720	Male, age 74, both hemispheres	1037.4
2123	Female, age 91, both hemispheres	626.6
2788	Male, age 74, unknown	452.1
2014	Male, age 55, unknown	401.0
2317	Female, age 72, unknown	387.7
2162	Male, age 80, both hemispheres	336.6
1980	Male, age 76, both hemispheres	253.5

Medial parabrachial nucleus
nTPM: 403.9

2156	Male, age 61, both hemispheres	856.6
2854	Male, age 80, both hemispheres	548.4
2786	Male, age 76, both hemispheres	258.9
2170	Female, age 91, both hemispheres	215.2
2463	Female, age 85, right hemisphere	140.2

Medial periolivary nuclei
nTPM: 621.8

2171	Female, age 85, both hemispheres	1147.3
2063	Male, age 76, both hemispheres	687.8
2458	Female, age 91, both hemispheres	554.5
2791	Male, age 74, right hemisphere	432.9
2081	Male, age 80, both hemispheres	286.5

Motor facial nucleus
nTPM: 665.5

2327	Male, age 80, both hemispheres	818.4
2697	Female, age 85, both hemispheres	818.3
2365	Male, age 74, right hemisphere	797.2
2062	Male, age 76, both hemispheres	688.9
2795	Female, age 91, both hemispheres	519.3
2126	Male, age 61, both hemispheres	350.8

Motor trigeminal nucleus
nTPM: 420.5

2079	Male, age 80, both hemispheres	569.9
2560	Male, age 74, both hemispheres	498.3
2321	Female, age 91, both hemispheres	429.8
2335	Male, age 61, both hemispheres	335.2
2309	Male, age 76, both hemispheres	269.3

Nuclei of the trapezoid body
nTPM: 713.5

2159	Male, age 61, both hemispheres	977.9
2735	Female, age 85, both hemispheres	682.0
1983	Male, age 76, both hemispheres	662.4
2368	Female, age 91, both hemispheres	640.5
2166	Male, age 80, both hemispheres	604.5

Nucleus raphe magnus
nTPM: 892.2

2455	Male, age 74, both hemispheres	1196.8
2172	Female, age 85, both hemispheres	1189.4
2160	Male, age 61, both hemispheres	1128.7
2328	Male, age 80, both hemispheres	757.4
2459	Female, age 91, both hemispheres	627.6
2051	Male, age 76, both hemispheres	453.5

Paramedian reticular nucleus
nTPM: 473.4

2050	Female, age 85, both hemispheres	582.4
2313	Male, age 61, both hemispheres	546.3
2057	Male, age 80, both hemispheres	440.5
2052	Male, age 76, both hemispheres	324.4

Pedunculopontine tegmental nucleus
nTPM: 275.2

2334	Male, age 80, both hemispheres	352.0
2338	Male, age 61, both hemispheres	295.4
1921	Female, age 85, both hemispheres	178.2

Pontine nuclei
nTPM: 566.1

2787	Female, age 85, both hemispheres	745.0
1863	Male, age 55, unknown	728.3
2727	Male, age 61, right hemisphere	686.9
2454	Male, age 74, left hemisphere	620.1
1968	Male, age 76, left hemisphere	576.8
2109	Female, age 72, unknown	483.8
2115	Male, age 80, left hemisphere	367.6
2319	Female, age 91, both hemispheres	320.5

Pontine raphe nucleus
nTPM: 303.6

2122	Female, age 85, midline	484.8
2853	Male, age 76, midline	122.3

Posteroventral cochlear nucleus
nTPM: 329.7

2752	Female, age 85, both hemispheres	482.7
2070	Male, age 76, both hemispheres	435.2
2371	Male, age 61, both hemispheres	404.2
2341	Male, age 80, both hemispheres	295.4
2135	Female, age 91, both hemispheres	31.2

Principal sensory trigeminal nucleus
nTPM: 936.1

2324	Male, age 76, both hemispheres	1583.6
2158	Male, age 61, both hemispheres	1059.2
2367	Female, age 91, left hemisphere	558.1
2008	Male, age 80, left hemisphere	543.6

Reticular pontine nucleus, caudal
nTPM: 554.4

2332	Male, age 80, right hemisphere	1003.4
2457	Female, age 91, both hemispheres	567.0
2092	Male, age 76, both hemispheres	458.9
2559	Male, age 74, both hemispheres	188.4

Reticular pontine nucleus, oral
nTPM: 414.0

2361	Male, age 74, both hemispheres	725.1
2366	Female, age 91, both hemispheres	482.5
2012	Female, age 85, both hemispheres	359.0
2167	Male, age 76, both hemispheres	297.0
1939	Male, age 80, both hemispheres	206.2

Reticulotegmental nucleus
nTPM: 625.0

2322	Female, age 91, both hemispheres	840.9
2333	Male, age 80, both hemispheres	601.9
2325	Male, age 76, both hemispheres	570.8
2452	Male, age 74, both hemispheres	486.4

Spinal trigeminal nucleus, oral
nTPM: 927.0

2164	Male, age 80, both hemispheres	1653.3
2737	Female, age 85, both hemispheres	840.2
1978	Male, age 76, both hemispheres	287.7

Subcoeruleus area
nTPM: 325.0

2089	Male, age 76, left hemisphere	483.6
1958	Male, age 80, both hemispheres	404.1
2323	Female, age 91, left hemisphere	367.9
2451	Male, age 74, both hemispheres	219.5
2369	Female, age 85, left hemisphere	149.8

Superior olive
nTPM: 568.8

2329	Male, age 80, right hemisphere	678.0
2561	Female, age 91, both hemispheres	606.8
1875	Female, age 85, both hemispheres	589.7
2364	Male, age 74, right hemisphere	564.9
2020	Male, age 76, both hemispheres	404.6

Ventral periolivary nuclei
nTPM: 654.5

2165	Male, age 80, both hemispheres	908.8
2794	Female, age 91, left hemisphere	694.2
2130	Female, age 85, both hemispheres	663.4
2023	Male, age 76, both hemispheres	351.6

Ventrolateral tegmental area, A5 NE cell group
nTPM: 567.1

2449	Male, age 74, both hemispheres	987.1
2840	Female, age 85, both hemispheres	810.3
2161	Male, age 80, both hemispheres	521.0
1959	Male, age 76, both hemispheres	454.4
2456	Female, age 91, both hemispheres	422.2
2359	Male, age 61, both hemispheres	207.5

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.	2197.6

FANTOM5 sample id

Sample description

Scaled Tags Per Million

Locus coeruleus
Scaled Tags Per Million: 1139.7

FF:10182-103D2	60 years, female	1913.6
FF:10165-103B3	76 years, female	365.8

Pons
Scaled Tags Per Million: 2197.6

FF:10033-101E6

18-54 years, mixed

2197.6

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.	304.2

Rat sample

Sample description

nTPM

Pons
nTPM: 304.2

Samples: 4

Max nTPM: 356.9
Min nTPM: 242.1

Sample A		356.9
Sample A		303.1
Sample A		242.1
Sample A		314.6