 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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 |
| 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) |
| 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 |
|
| Relations |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
