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Series GSE43366 Query DataSets for GSE43366
Status Public on Jul 15, 2013
Title Defining the microglia transcriptome during disease progression in ALS transgenic mice
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: We purified spinal cord microglia utilizing percoll gradients and magnetic beads, followed by transcriptome profiling (RNA-seq) to define microglia expression profiles against other neural, immune cell-types. We next observed how the microglai transcriptomes change during activation in the SOD1-G93A mouse model of motor neuron degeneration at 3 timepoints. We also compared these profiles with that induced by LPS injection.
Results and conclusions: ALS microglia were found to differ substantially from those activated by LPS and from M1/M2 macrophages by comparison with published datasets. These ALS microglia showing substantial induction of a "neurodegeneration-tailored phenotype", with induction of lysosomal, RNA splicing, and Alzheimer's disease pathway genes. Overall they express a mixture of neuroprotective and neurotoxic factors during activation in ALS mice, showing that neuro-immune activation in the spinal cord is a double-edged sword. We also detected the transcriptional nature of surface marker expression in microglia (CD11b, CD86, CD11c), and substantial T-cell microglia cross-talk using correlative microglia transcriptome/FACS analysis.
Overall design 42 total RNA samples from purified spinal cord microglia were subjected to paired-end RNA-sequencing. Parallel flow cytometry data was collected from the same spinal cords.
Contributor(s) Chiu IM, O'Keeffe S, Maniatis T
Citation(s) 23850290
Submission date Jan 08, 2013
Last update date May 15, 2019
Contact name Sean O'Keeffe
Organization name Columbia University
Street address 701 West 168th Street
City New York
ZIP/Postal code 10032
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (42)
GSM1061143 SOD1G93A_Day65_A
GSM1061144 SOD1G93A_Day65_B
GSM1061145 SOD1G93A_Day65_C
SRA SRP017849
BioProject PRJNA185990

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE43366_microglia_processed_RPKM.txt.gz 2.9 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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