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SRX11908886: GSM5536817: MUC26004; Mus musculus; OTHER
8 ILLUMINA (Illumina NovaSeq 6000) runs: 57.3M spots, 6.7G bases, 1.9Gb downloads

Submitted by: NCBI (GEO)
Study: Single cell analysis of meningeal ectopic lymphoid tissue and secondary lymphoid tissues in a spontaneous EAE model
PRJNA757745 • SRP334107 • All experiments • All runs
show Abstracthide Abstract
Objective: To investigate how similar meningeal ectopic lymhpoid tissue (mELT) is to secondary lymphoid tissues and find unique features of mELT that could allow therapeutic targetting of mELT specifically. Methods: We utilized a spontaneous chronic experimental autoimmune encephalomyelitis (EAE) model of mice with mutant T and B cell receptors specific for myelin oligodendrocyte glycoprotein (MOG), which develop meningeal inflammatory infiltrates resembling those described in Multiple Sclerosis (MS). We identified differences in cell composition and gene expression between mELT and secondary lymphoid tissues (lumbar and inguinal lymph nodes and the spleen) using single cell sequencing. Overall design: single cell gene expression and Bcell receptor sequences of meningeal ectopic lymphoid tissue, blood, spleen, inguinal and lumbar lymph nodes in 3 Thx2D2 mice
Sample: MUC26004
SAMN20972356 • SRS9919777 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina NovaSeq 6000
Strategy: OTHER
Source: TRANSCRIPTOMIC
Selection: other
Layout: PAIRED
Construction protocol: Blood was collected by cardiac puncture. After thorough perfusion with PBS the spleen, inguinal lymph nodes, lumbar lymph nodes and spinal cord were dissected, and meninges were detached from the spinal cord using fine forceps. Organs were passed through cell strainers. Erythrocyte lysis was performed for spleen and blood. Samples were enriched for CD45+ cells using a MACS (Miltenyi Biotech) with anti‐CD45 mouse MAb‐conjugated microbeads (Miltenyi Biotech, #130-052-301). Fc receptors were blocked and samples were incubatedwith DNA barcoded TotalSeq antibodies against CD4 (TotalSeq-C0001 anti-mouse CD4, clone RM4-5, Biolegend), CD8a (TotalSeq-C0002 anti-mouse CD8a , clone 53-6.7, Biolegend), CD19 (TotalSeq-C0093 anti-mouse CD19, clone 6D5, Biolegend), Ly6G (TotalSeq-C0015 anti-mouse Ly6G , clone 1A8, Biolegend), and NK1.1 (TotalSeq-C0118 anti-mouse NK-1.1, clone PK136, Biolegend), and one of 2 TotalSeq Hashtag antibodies (TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody, clones M1/42; 30-F11, Biolegend or TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody, clones M1/42; 30-F11, Biolegend), to allow pooling of 2 samples per experiment. 10x Genomics Chromium Next GEM Single Cell V(D)J Reagent Kit (v1.1)
Experiment attributes:
GEO Accession: GSM5536817
Links:
Runs: 8 runs, 57.3M spots, 6.7G bases, 1.9Gb
Run# of Spots# of BasesSizePublished
SRR156117067,114,177832.4M241Mb2023-11-01
SRR156117077,208,290843.4M243.4Mb2023-11-01
SRR156117086,139,989718.4M207.1Mb2023-11-01
SRR156117096,252,355731.5M210.3Mb2023-11-01
SRR156117107,109,033831.8M240.8Mb2023-11-01
SRR156117117,192,156841.5M242.9Mb2023-11-01
SRR156117128,076,293944.9M273.6Mb2023-11-01
SRR156117138,178,285956.9M276.3Mb2023-11-01

ID:
15827001

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