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Sample GSM5678417 Query DataSets for GSM5678417
Status Public on Apr 12, 2023
Title SC_EAE14
Sample type SRA
 
Source name spinal cord
Organism Mus musculus
Characteristics strain: C57Bl/6J
tissue: spinal cord
eae disease stage: EAE peak
Treatment protocol Naïve mice were left untreated. Wild-type mice were induced with EAE by active immunization with MOG35-55.
Extracted molecule polyA RNA
Extraction protocol Mice were perfused with ice-cold PBS and the brain, SC, cranial dura, and spinal dura were dissected. For the cranial and spinal dura, after enzymatic digestion with Collagenase VIII and DNaseI and mechanical dissociation, cells were pre-incubated with mouse Fc Blocker (clone 2.4G2, BD Pharmingen), and then stained with CD45-FITC (clone 30-F11, BioLegend), CD31-APC (clone MEC13.3, BD Pharmingen), and DAPI. For the brain and SC, after enzymatic digestion, mechanical dissociation and myelin debris removal, cells were pre-incubated with mouse Fc Blocker, and then stained with CD45-FITC, CD31-APC, and DAPI. Approximately 1:1~3:1 of viable DAPI-CD45+ immune cells and DAPI-CD31+ endothelial cells were sorted with BD Influx Cell Sorter (BD Biosciences) into PBS supplemented with 0.04% BSA.
Libraries were prepared according to 10XGenomics's instructions.
Sample libraries were sequenced on the Illumina NovaSeq 6000 system.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description EAE mice at 14 dpi
Data processing The Cell Ranger v 6.0 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10.
We used the Seurat R package (v4.0.4) for QC, filtering and analysis of the filtered data (Hao et al. Cell 2021).
Cells were filtered based on nfeature_RNA, nCount_RNA, and the percentage of mitochondrial genes.
Genome_build: mm10
 
Submission date Nov 08, 2021
Last update date Apr 13, 2023
Contact name Zhilin Li
E-mail(s) zhilin.li@outlook.com
Organization name University of Helsinki
Street address Haartmaninkatu 8
City Helsinki
ZIP/Postal code 00290
Country Finland
 
Platform ID GPL24247
Series (1)
GSE168202 Single cell RNA-seq analysis of the transcriptomic profiles of endothelial cells and immune cells from the brain, spinal cord (SC), dorsal cranial dura, and spinal dura of naïve and EAE mice at the onset and peak of the disease
Relations
BioSample SAMN22978665
SRA SRX13041640

Supplementary file Size Download File type/resource
GSM5678417_SC_EAE14_barcodes.tsv.gz 41.3 Kb (ftp)(http) TSV
GSM5678417_SC_EAE14_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSM5678417_SC_EAE14_matrix.mtx.gz 78.2 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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