Single-cell RNAseq for glia
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5 weeks ago
genetics78 • 0

Hi,

I was wondering if anyone knew where I could find single-cell RNAseq data for oligodendrocytes (preferably human but could also be mouse).

RNA-Seq rna-seq sequencing • 190 views
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5 weeks ago
jaro.slamecka ▴ 140

One option is the recently published atlas of human tissues: https://descartes.brotmanbaty.org/ It includes oligodendrocytes and was derived using sci-RNA-seq3 (three-level combinatorial indexing). The link points to the interactive tool for exploration. Tables and some data can be downloaded from there directly (raw data on dbGaP). Related publication: 10.1126/science.aba7721 https://science.sciencemag.org/content/370/6518/eaba7721.long

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Thank you so much for your help! I will check this out.

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5 weeks ago

Hey @genetics78,

The NCBI GEO is usually my go-to for searching for data.

I searched oligodendrocytes and then clicked Datasets selected to filter by humans on right hand side.

I found one interesting dataset.

Developmental trajectory of oligodendrocyte progenitor cells in the human brain revealed by single cell RNA sequencing https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE155488

I could also bet that some of the other datasets that say whole-brain scRNA-seq or maybe even multiple organ types scRNA-seq, could also include oligodendrocytes within their datasets. You may just have to subset the data to get a focus on the brain/oligodendrocytes.

EDIT: Oh yes, I realized @jaro.slamecka posted the same resource below.

Here's one of multiple human fetal tissues:

A human cell atlas of fetal gene expression https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE156793

with a companion dataset of: A human cell atlas of fetal chromatin accessibility https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149683

Here is the associated web atlas (it was kind of slow for me, might be my computer): https://atlas.brotmanbaty.org/

Good luck!

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Hey Pancreas Pratik, Thank you so much for your help! I will check these links. The https://atlas.brotmanbaty.org/ is also very slow on my computer unfortunately.