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| Status |
Public on Aug 31, 2023 |
| Title |
HA844, oligodendrocyte co-cultured in direct with T cells (TCO), scRNAseq |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain
cell type_1: primary Oligodendrocytes
cell type_2: T cells
treatment: Direct contact co-culture with T cells (TCO) for 12 hours
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| Growth protocol |
OLs were isolated from fresh non-pathological brain tissue from surgical resections for non-tumoral intractable focal epilepsy as previously published (Rone MB et al., 2016). OLs were harvested and plated on poly-L-lysine and extracellular matrix coated wells. During the first 4 days, OLs were allowed to grow in enriched cell medium containing 2ng/mL T3 , 1/50 N1 supplement , 1/50 B27 , 10ng/mL basic fibroblast growth factor and 10ng/mL platelet derived growth factor – AA as previously published (Rone MB et al., 2016). After cell process extension, fresh medium without basic fibroblast growth factor and platelet derived growth factor – AA was used. Cells were treated with the experimental conditions after 8-10 days in vitro
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| Extracted molecule |
total RNA |
| Extraction protocol |
In brief, media was collected and cells were treated with PBS-EDTA to detach the oligodendrocytes from the bottom of the well. Once cells were visibly detached, the suspension was combined with the collected media and the wells were washed twice with PBS to collect any residual cells and transferred to the same sample tube. The samples were centrifuged at 800rpm for 10min to pellet the live cells and then resuspended in PBS at a concentration of 350 thousand cells per milliliter. Approximately 10,000 cells were used for library construction.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
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| Submission date |
Apr 28, 2023 |
| Last update date |
Aug 31, 2023 |
| Contact name |
Haritha Desu |
| E-mail(s) |
desuharitha5@gmail.com
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| Organization name |
Centre de recherche du Centre Hospitalier de l'Université de Montréal
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| Department |
Neurosciences
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| Street address |
900 R. Saint-Denis
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| City |
Montreal |
| State/province |
Québec |
| ZIP/Postal code |
H2X 0A9 |
| Country |
Canada |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE230828 |
Activated leukocyte cell adhesion molecule on human oligodendrocytes mediates Th17 cell adhesion |
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| Relations |
| BioSample |
SAMN34415094 |
| SRA |
SRX20124971 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7244790_HA844_TCO_barcodes.tsv.gz |
146.9 Kb |
(ftp)(http) |
TSV |
| GSM7244790_HA844_TCO_features.tsv.gz |
297.6 Kb |
(ftp)(http) |
TSV |
| GSM7244790_HA844_TCO_matrix.mtx.gz |
206.2 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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