Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species
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PRJNA513835

PRJNA513835: Single-cell RNA-seq in monozygotic twins discordant for multiple sclerosis

Source: NCBI / GSE127969
Submission Date: Mar 06 2019
Release Date: Aug 02 2019
Update Date: Nov 01 2019

Summary: Here we investigated the earliest possible evidence of subclinical neuro-inflammation (SCNI) using a small cohort of monozygotic twins where one sibling had clinically definite MS and the other been clinically "healthy" but has a maximal genetic for developing MS. In contrast to subjects with radiologically isolated syndrome (RIS), our group of very early SCNI does not even fulfill the (arbitrary) MRI criteria for RIS but have more subtle MRI changes and/or evidence of neuro-inflammation in the CSF, e.g. oligoclonal bands (OCBs). For analyzing CSF samples from Twin pairs and controls in greater detail we applied single-cell whole transcriptome sequencing (scRNAseq). Our findings demonstrate that even the earliest experimentally approachable stage of MS is characterized by synergistic activation of CD8+ T cells, CD4+ T cells and B cells.

Overall Design: scRNA-seq. Library preparation: Smart-seq2; alignement: to UCSC hg38 using HISAT2; gene counts: featureCounts (Liao et al.); single-cell analysis: Seurat // PRJNA513835 - SRP180896

GEN Datasets:
GEND000033
Strategy:
Species:
Tissue:
Healthy Condition:
Cell Type:
Protocol
Growth Protocol: -
Treatment Protocol: -
Extract Protocol: Smart-seq2
Library Construction Protocol: -
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: -
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 1500
Strand-Specific: Unspecific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate
Publications
Early adaptive immune activation detected in monozygotic twins with prodromal multiple sclerosis.
The Journal of clinical investigation . 2019-11-01 [PMID: 31566584]