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Sample GSM3693381 Query DataSets for GSM3693381
Status Public on Mar 10, 2020
Title ECA2
Sample type SRA
Source name Spinal cord immune cells and endothelial cells
Organism Mus musculus
Characteristics strain: C57Bl/6JCrl
protocol: Endothelial cell-specific Ang2-overexpressing mice were induced with EAE.
age: 12-14 weeks
tissue: Spinal cord
Treatment protocol For sample 1 and 2, wild-type mice were induced with EAE by immunization with MOG35-55 emulsified in CFA and treated with antibodies prophylacticly starting at the time of EAE induction for two weeks. For Sample 3 and 4, mice were induced with EAE by immunization with MOG35-55 emulsified in CFA.
Extracted molecule polyA RNA
Extraction protocol Single cells from spinal cords were isolated for single-cell RNA-sequencing as described previously (Vanlandewijck et al. Nature 2018). Mice were perfused with ice-cold PBS and spinal cords were dissected. Briefly, after enzymatic digestion, mechanical dissociation and myelin debris removal, eluted cells were incubated with mouse Fc Blocker (clone 2.4G2, BD Pharmingen) stained with CD45-FITC (clone 30-F11, BioLegend), CD31-APC (clone MEC13.3, BD Pharmingen), and DAPI. Equal numbers of viable DAPI-CD45+ leukocytes and DAPI-CD31+ ECs were sorted with BD Influx Cell Sorter (BD Biosciences) into PBS supplemented with 0.04% BSA.
Subsequent cDNA purification, amplification (12 cycles) and library construction (sample index PCR 14 cycles) was performed as instructed.
Sample libraries were sequenced on the Illumina NovaSeq 6000 system using S1 flow cell (Illumina)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description Endothelial cell-specific Ang2-overexpressing mice were induced with EAE.
Data processing The Cell Ranger v 2.1.1 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 (v2.3.4) for QC, filtering and analysis of the aggregated data (Butler et al. Nature Biotechnology 2018)
Cells were filtered based on the number of genes and the percentage of mitochondrial genes.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx
Submission date Apr 01, 2019
Last update date Mar 30, 2022
Contact name Zhilin Li
Organization name University of Helsinki
Street address Haartmaninkatu 8
City Helsinki
ZIP/Postal code 00290
Country Finland
Platform ID GPL24247
Series (1)
GSE129105 Single cell RNA-seq data in the immune cells and endothelial cells isolated from spinal cord of EAE mice upon Ang2 blockade and overexpression
BioSample SAMN11298834
SRA SRX5611105

Supplementary file Size Download File type/resource
GSM3693381_ECA2_barcodes.tsv.gz 2.2 Mb (ftp)(http) TSV
GSM3693381_ECA2_genes.tsv.gz 212.7 Kb (ftp)(http) TSV
GSM3693381_ECA2_matrix.mtx.gz 59.6 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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