GSE107451 Aging Drosophila Brain

A single-cell transcriptome atlas of the ageing Drosophila melanogaster brain (Davie et al., Cell 2018). Analysis here uses the annotated 57k 10x atlas (GSE107451_57k_10x_counts.h5ad; DGRP-551 and w¹¹¹⁸; 0 / 1 / 3 / 6 / 9 / 15 / 30 / 50 days) with the authors' cell-type labels, QC, Leiden clustering, UMAP and an Old (30–50 d) vs Young (0–3 d) comparison.

Species Fruit fly (Drosophila melanogaster) Tissue Whole brain Journal Cell (2018) PMID 29909982 ↗ GEO GSE107451 ↗ DataID Data1192

56902cells after QC

14463genes

75named cell types

9046 / 29240Old / Young cells

UMAP overview

Left→right: Leiden clusters · cell class (paper labels collapsed) · age group · genotype. Young = 0–3 days, Mid = 6–15 days, Old = 30–50 days.

Cell classes and paper annotations

The GEO 57k metadata carries the Davie atlas labels (Kenyon cells, glia, optic-lobe neurons, neuromodulatory types). Numeric labels are unannotated Seurat clusters kept as Unannotated.

Cell class	Cells	Young %	Mid %	Old %
Glia	3739	4.6	5.3	15.6
Hemocyte	329	0.3	0.7	1.1
Kenyon_cell	2848	5.8	4.8	3
Neuron	13891	27.6	23.3	16.4
Photoreceptor	277	0.5	0.3	0.7
Unannotated	35818	61.2	65.7	63.1

Age (days)	Cells
0	12105
1	9173
3	7962
6	8527
9	5762
15	4327
30	6062
50	2984

Named cell type	Class	Cells	Young	Mid	Old
G-KC	Kenyon_cell	1642	1012	430	200
Ensheathing_glia	Glia	1517	660	423	434
Astrocyte-like	Glia	1421	364	306	751
TmY14	Neuron	1399	953	336	110
Pm1/Pm2	Neuron	1162	806	276	80
Mip	Neuron	814	359	323	132
A/B-KC	Kenyon_cell	688	394	256	38
Hsp	Neuron	668	654	14	0
T4/T5	Neuron	648	462	168	18
Mi1	Neuron	562	293	177	92
A/B*-KC	Kenyon_cell	518	285	201	32
T2	Neuron	507	338	151	18
T3	Neuron	471	306	144	21
T1	Neuron	428	185	231	12
Serotonergic	Neuron	391	184	148	59
Clock	Neuron	389	183	147	59
Tm5c	Neuron	382	142	146	94
Tm5ab	Neuron	351	187	141	23
Plasmatocytes	Hemocyte	329	102	123	104
Tm1/TmY8	Neuron	325	191	88	46
Pm1/Pm2/Pm3	Neuron	316	191	93	32
Lamina_monopolar	Neuron	307	161	123	23
Photoreceptors	Photoreceptor	277	148	62	67
Dm8/Dm11	Neuron	276	175	84	17
Pm4	Neuron	271	207	48	16
Perineurial_glia	Glia	259	103	111	45
MBON	Neuron	257	47	171	39
Lawf1	Neuron	246	143	76	27
Cortex_glia	Glia	239	115	44	80
dorsal_Fan-shaped_Body	Neuron	232	158	66	8

⬇ Download annotated h5ad (56,902 × 14,463)

Composition across the lifespan

Paper finding: neuronal identity is largely retained; glial / support compartments remodel as RNA content declines with age. Stacked bars show class fractions by binned age and by exact day.

Differential expression — Old vs Young

Wilcoxon rank-sums on all cells (Old 30–50 d vs Young 0–3 d); top 50 up/down by adjusted p-value. Consistent with the paper, neuronal identity markers persist while mitochondrial / heat-shock transcripts fall and ribosomal / translation genes rise in old brains.

Up in Old (aged ↑)

Gene	log2FC	padj
eEF1alpha1	1.78	0.0e+0
RpL22	1.54	0.0e+0
sta	2.05	0.0e+0
MRE16	1.8	0.0e+0
Msp300	0.8	4.9e-270
Xrp1	1.7	1.6e-231
cib	1.53	5.9e-133
Fer1HCH	0.13	1.8e-120
CR40469	2.09	6.5e-99
CG10433	2.4	9.6e-97
CG5758	1.07	1.1e-95
vir-1	2.2	4.7e-92

Down in Old (aged ↓)

Gene	log2FC	padj
mt:lrRNA	-2.17	0.0e+0
DnaJ-1	-2.4	0.0e+0
jdp	-1.49	0.0e+0
mt:ND5	-1.08	0.0e+0
Cbp53E	-1.57	0.0e+0
Hsp26	-2.32	0.0e+0
Hsp83	-1.25	0.0e+0
igl	-1.17	6.1e-298
VAChT	-1.14	2.0e-255
Hsp70Bc	-2.03	1.4e-238
CG11000	-1	1.6e-235
Dop2R	-1.08	4.6e-196

Hallmark ageing genes (Imp · stress · glia)

Imp (IGF-II mRNA-binding protein) is plotted with antioxidant, heat-shock and glial markers on the same age trajectory. In this 57k matrix Imp is highest in Kenyon cells and rises further in old KC / neurons; Hsp83 and GstD1 fall after mid-life.

Age	Class	Imp	Sod2	Cat	GstD1	GstE1	GstS1	GstD2	Hsp70Bb	Hsp70Ba	Hsp83	Hsp26	Hsp27	Thor	foxo	InR	chico	Ilp2	Ilp3	Ilp5	repo	alrm	wrapper	moody	elav	nSyb	Appl	Syt1	brp	Mmp1	daw	tobi	RpL3	RpS3	RpL32	eEF1alpha1	sn	Hsromega
Mid	Glia	0.522	0.626	0.213	1.476	0.78	0.203	0.044	0.006	0.003	1.368	0.286	0.158	0.219	0.308	1.288	0.094	0.004	0.002	0.002	0.839	2.062	0.08	0.255	0.483	0.457	0.389	0.428	0.252	0.181	0.125	0.002	2.152	2.042	2.882	2.514	0.042	2.753
Mid	Hemocyte	0.614	0.425	0.463	0.428	0.35	0.161	0.02	0.003	0.014	2.012	1.033	0.624	0.58	0.243	0.738	0.115	0	0	0	0.039	0.109	0	0.033	0.719	1.108	1.025	0.95	0.385	0.015	0.011	0	2.814	2.377	2.923	3.058	0.118	2.813
Mid	Kenyon_cell	1.582	0.481	0.091	0.516	0.018	0.019	0.002	0.042	0.035	2.544	2.13	1.12	0.006	0	0.372	0.09	0	0	0.003	0.007	0.078	0.002	0	1.77	2.948	3.282	2.253	1.677	0.006	0	0	1.797	1.771	2.452	0.369	0.166	4.029
Mid	Neuron	0.403	0.712	0.089	0.108	0.008	0.04	0.001	0.014	0.011	1.914	1.13	0.457	0.011	0.03	0.576	0.103	0.018	0.008	0.007	0.009	0.091	0.004	0.004	1.429	2.919	2.41	2.573	1.143	0.009	0.001	0.004	2.098	1.785	2.396	0.846	0.187	3.878
Mid	Photoreceptor	0.428	0.835	0.147	0.265	0.031	0.155	0.185	0	0.013	1.38	0.774	0.311	0.441	0.082	0.756	0.034	0	0.007	0	0.099	0.141	0.032	0	0.79	2.434	1.94	2.169	1.01	0	0	0.018	2.194	1.736	2.338	1.098	0.149	3.67
Mid	Unannotated	0.523	0.628	0.075	0.086	0.013	0.036	0.003	0.017	0.016	1.951	1.345	0.63	0.017	0.015	0.712	0.095	0.013	0.003	0.003	0.011	0.089	0.004	0.006	1.421	2.778	2.252	2.423	1.208	0.006	0.002	0.001	2.188	1.655	2.225	0.819	0.308	4.266
Old	Glia	0.512	0.481	0.273	0.135	1.438	0.241	0.086	0.015	0	0.912	0.063	0.042	0.179	0.197	1.012	0.056	0.006	0	0.006	0.706	2.392	0.16	0.214	0.447	0.377	0.299	0.341	0.181	0.428	0.075	0	2.172	1.613	2.571	2.782	0.04	1.936
Old	Hemocyte	0.651	0.587	0.87	0.059	0.609	0.272	0.016	0.008	0	1.382	0.448	0.351	0.259	0.171	0.708	0.076	0.037	0	0	0.026	0.209	0	0.105	0.759	1.181	0.976	1	0.54	0.128	0.037	0	2.151	1.69	2.36	2.745	0.127	2.084
Old	Kenyon_cell	2.142	0.359	0.073	0	0.029	0.022	0	0.055	0.006	1.181	0.75	0.506	0.006	0.007	0.391	0.069	0	0	0	0	0.113	0.014	0.028	1.761	2.818	3.23	2.043	1.59	0.006	0	0	1.672	1.332	1.847	0.614	0.06	2.834
Old	Neuron	0.65	0.585	0.147	0.015	0.032	0.092	0.002	0.028	0.004	1.252	0.48	0.285	0.012	0.033	0.545	0.067	0.008	0.002	0.006	0.011	0.131	0.002	0.006	1.307	2.823	2.357	2.417	1.17	0.01	0.005	0.001	2.133	1.376	2.058	1.21	0.261	3.121
Old	Photoreceptor	0.679	0.686	0.136	0.043	0.053	0.068	0.021	0	0	1.103	0.379	0.193	0.209	0	0.598	0.076	0.027	0	0	0.043	0.177	0	0.021	0.898	2.916	1.939	1.985	0.822	0.031	0	0	1.892	1.493	1.837	1.066	0.198	2.982
Old	Unannotated	0.705	0.517	0.099	0.014	0.054	0.068	0.014	0.023	0.002	1.249	0.468	0.228	0.014	0.018	0.651	0.072	0.014	0.005	0.009	0.018	0.161	0.011	0.006	1.322	2.606	2.232	2.329	1.069	0.016	0.002	0	2.286	1.329	2.048	1.19	0.312	3.137
Young	Glia	0.519	0.66	0.178	0.877	1.038	0.304	0.013	0.011	0.005	0.957	0.482	0.152	0.224	0.217	0.904	0.079	0.028	0.012	0.036	0.838	2.265	0.202	0.4	0.563	0.987	0.647	0.815	0.397	0.137	0.101	0.002	1.979	1.923	2.308	2.571	0.092	3.127
Young	Hemocyte	0.587	0.687	0.5	0.16	0.299	0.035	0	0.013	0	2.011	1.08	0.545	0.658	0.283	0.746	0.11	0.033	0.015	0	0.008	0.155	0.005	0.059	0.999	1.787	1.26	1.544	0.737	0.05	0	0	2.331	2.052	2.574	2.286	0.177	3.41
Young	Kenyon_cell	1.715	0.639	0.07	0.474	0.014	0.01	0	0.02	0.017	2.392	1.694	0.668	0.004	0.002	0.299	0.081	0.038	0.017	0.017	0.013	0.155	0.004	0.005	1.753	3.123	3.365	2.474	1.781	0.006	0.002	0	1.649	1.661	2.1	0.4	0.19	4.018
Young	Neuron	0.303	0.811	0.096	0.099	0.018	0.028	0.001	0.015	0.008	1.97	1.249	0.399	0.017	0.022	0.547	0.092	0.06	0.032	0.046	0.009	0.214	0.005	0.005	1.315	3.329	2.376	2.924	1.357	0.024	0.001	0.001	1.8	1.459	1.841	0.588	0.205	4.138
Young	Photoreceptor	0.416	0.766	0.098	0.168	0.008	0.114	0.022	0.019	0.046	2.27	1.955	0.766	0.279	0.01	0.517	0.032	0.049	0	0.053	0.005	0.227	0	0.021	1.037	3.241	2.167	2.562	1.273	0.024	0	0.009	1.976	1.635	1.951	0.568	0.232	4.157
Young	Unannotated	0.447	0.673	0.079	0.058	0.018	0.031	0.002	0.016	0.011	1.838	1.292	0.512	0.013	0.015	0.668	0.094	0.041	0.021	0.024	0.009	0.157	0.003	0.006	1.39	3.221	2.294	2.757	1.412	0.01	0.001	0.002	1.8	1.455	1.751	0.571	0.289	4.372

Cluster marker genes (top)

Wilcoxon marker genes per Leiden cluster; majority paper label shown for orientation.

Cluster	Majority label	Top markers
0	Unannotated	pros · CG31221 · VAChT · jeb · Ddc · trv · noe · IA-2 · spab · Dop2R
1	Unannotated	VGlut · CG32017 · CG34355 · IA-2 · CG2269 · Nplp1 · bru3 · Dop2R · noe · CG18467
2	Unannotated	CG14989 · Gad1 · CG32017 · Nplp1 · mbl · nAChRalpha7 · hth · shakB · Ald · CG12594
3	Unannotated	Imp · jeb · CG31221 · mamo · VAChT · spab · IA-2 · mbl · Msp300 · unc-13-4A
4	Unannotated	VAChT · CG31221 · Frq1 · SoxN · CG9650 · scro · Cbp53E · mamo · toy · eys
5	Unannotated	VGlut · CG34355 · CG32017 · Frq1 · Cngl · CG9650 · D · Eip63F-1 · Ald · Ets65A
6	G-KC	Pka-C1 · jdp · mub · Pka-R2 · mamo · Rgk1 · Pkc53E · Pka-C3 · Dop1R2 · prt
7	Unannotated	Hsp26 · Hsp70Bc · DnaJ-1 · Hsp23 · Hsp83 · Hsp27 · Hsp68 · CG31221 · alphagamma-element:CR32865 · pros
8	Ensheathing_glia	nrv2 · CG8369 · MRE16 · Ugt35b · Msr-110 · CG31706 · bnb · CG1552 · CG5758 · Sod3
9	Unannotated	Obp44a · CG8369 · CG14989 · Hsp26 · Hsp83 · DnaJ-1 · Hsp23 · Cbp53E · Ald · Hsp70Bc
10	Astrocyte-like	CG9394 · Gs2 · CG1552 · CG7607 · CG31705 · Gat · CAH1 · CG15209 · Msr-110 · alrm
11	Mi1	Pka-C3 · Tk · Mmp2 · Rbp6 · CG31221 · CG2016 · Octbeta1R · rdgA · Cbp53E · sosie
12	Tm5ab	Rbp6 · Cbp53E · scro · Tk · CG42541 · mbl · VAChT · Frq1 · ct · CG11000
13	Pm1/Pm2	CG14989 · Gad1 · CG13739 · Lim3 · heph · CG8861 · hth · mab-21 · CR45312 · CG11294
14	A/B-KC	mub · Pka-C1 · Pka-R2 · jdp · Pkc53E · sNPF · Rgk1 · CG13739 · rad · Rab27
15	Unannotated	eEF1alpha1 · MRE16 · CG15098 · vir-1 · Cys · GstE12 · AnxB9 · Aldh · Mdh1 · CG10550
16	T4/T5	SoxN · acj6 · Lim1 · CG14340 · Scp2 · Frq1 · zld · Fas3 · ST6Gal · CNMaR
17	C3	CG14989 · Gad1 · Eip63F-1 · Pka-C3 · Pvf3 · Nos · SoxN · CG33639 · Octbeta1R · CG13698
18	T3	nAChRalpha7 · acj6 · beat-IIa · Tk · Cbp53E · fkh · CG42541 · bi · beat-IIb · Drep3
19	Unannotated	CG43729 · hth · ST6Gal · mbl · igl · acj6 · otp · VAChT · mub · CG31221
20	Unannotated	vvl · nAChRalpha6 · CG9650 · beat-IIIc · CG42540 · CG42541 · scro · dpr1 · Vsx2 · pyd
21	T2	nAChRalpha6 · sosie · beat-Ic · acj6 · CG9896 · beat-Ib · dpr1 · Cbp53E · scro · rdgA
22	T1	CG14274 · Eaat1 · CG2016 · Octbeta2R · CG15522 · Rbp6 · CG11000 · Mmp2 · pum · CG9932
23	Unannotated	beat-Ic · beat-Ib · jeb · dpr1 · CG9650 · beat-Ia · toy · VAChT · CG4577 · CG31221
24	L4/L5	CG11000 · Rbp6 · CG18598 · scro · Cngl · CG10947 · VAChT · Rh7 · pum · mamo
25	Tm5c	CG42540 · CG2016 · CG34355 · nAChRalpha7 · Npc2a · CG1358 · bi · Scp2 · CG43729 · Pkc53E
26	Unannotated	CG4577 · Gpb5 · eEF1alpha1 · CG2269 · Nep1 · CG42394 · prt · Imp · IA-2 · CtsB1
27	Lawf1	Frq1 · hth · Eip63F-1 · Npc2a · igl · CG8641 · Cngl · Fas2 · CG42342 · CG43795
28	PAM	DAT · Vmat · Ddc · ple · Bx · hth · Dop2R · Fer2 · CG43729 · DIP-delta
29	Plasmatocytes	CG4250 · regucalcin · Karl · CG14629 · SPARC · Cp1 · CtsB1 · eEF1alpha1 · Col4a1 · CG34331
30	Dm9	VGlut · ort · CG8034 · SPR · Octbeta1R · Pdk · CG9932 · bru3 · rad · CR45312
31	Unannotated	nAChRalpha7 · br · pyd · dpr1 · acj6 · beat-IIIc · CR45223 · Ac78C · ST6Gal · bi
32	Unannotated	nAChRalpha6 · Tk · CG1402 · CG1688 · VGlut · pum · Lmx1a · CG34155 · CG43689 · caup
33	Tyraminergic	Vmat · Tdc2 · CG4577 · Lim1 · Dscam2 · pum · Imp · Sox21a · Rgk3 · Mmp2
34	AstA/Nplp1	AstA · Dat · IA-2 · CG32017 · CG10257 · CR45312 · CG14989 · beat-Ic · Gad1 · CG4577
35	AstA/NPF	CG15082 · NPF · AstA · CG43902 · CG7191 · Mmp2 · Nep1 · aop · pnt · Imp