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Sample GSM5536801 Query DataSets for GSM5536801
Status Public on Nov 01, 2023
Title MUC25988
Sample type SRA
 
Source name J119 BCR CSF+mELT
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
Treatment protocol mice were untreated
Growth protocol Thx2D2 mice develop spontaneous EAE with meningeal leukocytic infiltrates in the spinal cord. Mice were sacrificed 25±6 days after disease onset.
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)
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description VDJ-BCR
J119_filtered_contig_annotations.csv
J119_A_BCR
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
 
Submission date Aug 25, 2021
Last update date Nov 01, 2023
Contact name Gildas Lepennetier
E-mail(s) gildas.lepennetier@tum.de
Organization name Klinikum Rechts der Isar
Department Neurology
Street address Ismaninger Straße 22
City Munich
ZIP/Postal code 81675
Country Germany
 
Platform ID GPL24247
Series (1)
GSE182774 Single cell analysis of meningeal ectopic lymphoid tissue and secondary lymphoid tissues in a spontaneous EAE model
Relations
BioSample SAMN20972340
SRA SRX11908870

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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