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| Status |
Public on Apr 12, 2023 |
| Title |
brain_EAE10 |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6J
tissue: brain
eae disease stage: EAE onset
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| Treatment protocol |
Naïve mice were left untreated. Wild-type mice were induced with EAE by active immunization with MOG35-55.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
EAE mice at 10 dpi
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| 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
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| Submission date |
Nov 08, 2021 |
| Last update date |
Apr 13, 2023 |
| Contact name |
Zhilin Li |
| E-mail(s) |
zhilin.li@outlook.com
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| Organization name |
University of Helsinki
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| Street address |
Haartmaninkatu 8
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| City |
Helsinki |
| ZIP/Postal code |
00290 |
| Country |
Finland |
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| 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 |
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| Relations |
| BioSample |
SAMN22978660 |
| SRA |
SRX13041636 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5678413_brain_EAE10_barcodes.tsv.gz |
54.5 Kb |
(ftp)(http) |
TSV |
| GSM5678413_brain_EAE10_features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
| GSM5678413_brain_EAE10_matrix.mtx.gz |
94.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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