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Astrocytes Originated from Neural Stem Cells Drive Regenerative Remodeling of Pathologic CSPGs in Spinal Cord Injury

GSE264511 Homo sapiens (human) RNA-seq (gene expression) 14 samples Submitted 2024/09/20 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 14 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
14 samples: 4 × Control primary spinal astroyctes # vs 4 × Activated primary spinal astrocytes# vs 3 × Control NPC-derived astrocytes# vs 3 × Activated NPC-derived astrocytes#Groups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Astrocytes originated from neural stem cells drive the regenerative remodeling of pathologic CSPGs in spinal cord injuryStem cell reports · 2024
Summary (written by the submitters)
Neural degeneration is a hallmark of spinal cord injury (SCI). Multipotent neural precursor cells (NPCs) have the potential to reconstruct the damaged neuron-glia network due to their tri-lineage capacity to generate neurons, astrocytes and oligodendrocytes. However, astrogenesis is the predominant fate of resident or transplanted NPCs in the SCI milieu adding to the abundant number of residents astrocytes in the lesion.
Read the full summary ↓
How NPC-derived astrocytes respond to the inflammatory milieu of SCI, and the mechanisms by which they contribute to the post-injury recovery processes remain largely unknown. Here, we uncover that activated NPC-derived astrocytes exhibit distinct molecular signature that is immune modulatory and foster neurogenesis, neuronal maturity and synaptogenesis. Mechanistically, NPC-derived astrocytes perform regenerative matrix remodeling by clearing the inhibitory chondroitin sulfate proteoglycans (CSPGs) from the injury milieu through LAR and PTP- receptor mediated endocytosis and production of ADAMTS1 and ADAMTS9, while most resident astrocytes are pro-inflammatory and contribute to pathologic deposition of CSPGs. These novel findings unravel critical mechanisms of NPC-mediated astrogenesis in SCI repair.
Published in
Astrocytes originated from neural stem cells drive the regenerative remodeling of pathologic CSPGs in spinal cord injury
Hosseini SM, Nemati S, Karimi-Abdolrezaee S · Stem cell reports 2024 · PMID 39303705 · doi:10.1016/j.stemcr.2024.08.007
This dataset
Open GSE264511 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE264511_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1102877 and SRA study SRP503155. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39303705) ↗
Study design
4 × Control primary spinal astroyctes # vs 4 × Activated primary spinal astrocytes# vs 3 × Control NPC-derived astrocytes# vs 3 × Activated NPC-derived astrocytes#

Supports a between-group comparison across 14 samples.

How we read this: 4 replicated groups read from 14 sample titles; they account for 14 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
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