Meta-analysis of mouse transcriptomic studies supports a context-dependent astrocyte reaction in acute CNS injury versus neurodegeneration

Das, Sudeshna; Li, Zhaozhi; Noori, Ayush; Hyman, Bradley T.; Serrano-Pozo, Alberto

doi:10.1186/s12974-020-01898-y

Journal of Neuroinflammation

Table 1 Summary of publicly available mouse astrocyte transcriptomic datasets used in this study

From: Meta-analysis of mouse transcriptomic studies supports a context-dependent astrocyte reaction in acute CNS injury versus neurodegeneration

Label	Injury type	Comparison	N	Sex (n M/F)	Age	CNS region	Astrocyte isolation method	RNA method	Accession #	Ref.
LPS	Acute	LPS vs placebo	5/4	5M/4M	30–35 days	ctx+cc	FACS of Aldh1L1-eGFP+ cells	Microarray	GSE35338	[1]
MCAO-1	Acute	MCAO vs sham surgery	3/3	3M/3M	30–35 days	ctx+cc+hipp+str	FACS of Aldh1L1-eGFP+ cells	Microarray	GSE35338	[1]
MCAO-2	Acute	Transient MCAO ipsi- vs contra and control (no TMX)	3/3	NA	3–5 months	Hemibrain	Cx43-Cre-ERT/RiboTag	RNA-seq	GSE103783	[12]
SCI-1	Acute	SCI at T10 vs non-injured	4/4	4F/4F	2–4 months	Spinal cord	mGFAP-Cre-RiboTag	RNA-seq	GSE76097	[13]
SCI-2	Acute	SCI at T9 (hemi-and full transection vs non-injured)	9/3	9M/3M	12 weeks	Spinal cord	FACS of Aldh1L1-eGFP+ cells	RNA-seq	GSE96054	[14]
MPTP-24 h	Acute	MPTP vs vehicle (sac 24 h post-single i.p. inj.)	3/3	3F/3F	4–7 months	str	TRAP of Aldh1L1-eGFP-L10a	Microarray	https://doi.org/10.17632/ktgcp4mtk2.1	[15]
SOD1-G93A-1	Chronic	G93A SOD1 vs wt	4/3	NA	90 days	Spinal cord	FACS Aldh1L1-eGFP/G93A SOD1	Microarray	GSE111031	[16]
SOD1-G93A-2	Chronic	G93A SOD1 vs wt	3/3	3M/3M	120 days	Spinal cord	LCM of Aldh1L1+ cells	Microarray	GSE69166	[17]
SOD1-G37R	Chronic	G37R SOD1 vs wt	4/6	4M/6M	8 months	Spinal cord	TRAP of Aldh1L1-eGFP-L10a	RNA-seq	GSE74724	[18]
APPPS1-1	Chronic	APPswePS1dE9 vs wt	4/4	NA	15–18 months	Whole ctx	FACS with Glt-1 Ab	Microarray	GSE74615	[19]
APPPS1-2	Chronic	APPswePS1dE9 vs wt	4/4	NA	15–18 months	Whole ctx	FACS of GFAP-GFP cells	Microarray	GSE74614	[20]
APPPS1-3	Chronic	APPswePS1dE9-GFP vs wt-GFP	4/7	4M/7M	9 months	CA1 hipp	FACS of eGFP+ cells	RNA-seq	GSE108520	[21]
PS2APP-1	Chronic	PS2APP vs wt	4/5	2M2F/1M4F	13 months	Whole brain	FACS with GFAP Ab	RNA-seq	GSE75431	[22]
PS2APP-2	Chronic	PS2APP vs wt	5/5	NA	11.5 months	Whole brain	FACS with GFAP Ab	RNA-seq	GSE129770	[23]
P301S-tau	Chronic	hMAPT-P301S tau vs wt	5/6	5M/6M	6 months	Whole ctx	FACS with GFAP Ab	RNA-seq	GSE129797	[23]

Abbreviations: Ab antibody, Aldh1L1 aldehyde dehydrogenase 1 L1, APP amyloid-β precursor protein, CA1 cornus ammonis 1, cc corpus callosum, CNS central nervous system, ctx cortex, Cx43 connexin-43, eGFP enhanced green fluorescent protein, FACS fluorescence-activated cell sorting, GFAP glial fibrillary acidic protein, Glt1 glutamate transporter 1, i.p. intra-peritoneal, LCM laser capture microdissection, LPS lipopolysaccharide, MAPT microtubule-associated protein tau, MCAO middle cerebral artery occlusion, MPTP 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, PS1/2 presenilin 1/2, sac sacrifice, SCI spinal cord injury, SOD1 superoxide dismutase 1, TRAP translating ribosome affinity purification

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ISSN: 1742-2094

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