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GEO help: Mouse over screen elements for information. |
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Status |
Public on Nov 01, 2023 |
Title |
MUC25988 |
Sample type |
SRA |
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Source name |
J119 BCR CSF+mELT
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Organism |
Mus musculus |
Characteristics |
strain: Thx2D2 Sex: female concentration (ng/ul): 10.9443960346627 volume (ul): 1.5 i7 index: SI-GA-F8 tissue hto: CSF=HTO tag1, mELT=HTO tag2
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Treatment protocol |
mice were untreated
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Growth protocol |
Thx2D2 mice develop spontaneous EAE with meningeal leukocytic infiltrates in the spinal cord. Mice were sacrificed 25±6 days after disease onset.
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Extracted molecule |
total RNA |
Extraction 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)
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Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
VDJ-BCR J119_filtered_contig_annotations.csv J119_A_BCR
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Data processing |
Library strategy: BCR-seq cellranger-5.0.1 multi, refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0, refdata-gex-mm10-2020-A, default options Hashtag Oligo used described in file Feature_mouse_10x.csv Genome_build: GRCm38
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Submission date |
Aug 25, 2021 |
Last update date |
Nov 01, 2023 |
Contact name |
Gildas Lepennetier |
E-mail(s) |
gildas.lepennetier@tum.de
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Organization name |
Klinikum Rechts der Isar
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Department |
Neurology
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Street address |
Ismaninger Straße 22
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City |
Munich |
ZIP/Postal code |
81675 |
Country |
Germany |
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Platform ID |
GPL24247 |
Series (1) |
GSE182774 |
Single cell analysis of meningeal ectopic lymphoid tissue and secondary lymphoid tissues in a spontaneous EAE model |
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Relations |
BioSample |
SAMN20972340 |
SRA |
SRX11908870 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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