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Series GSE89960 Query DataSets for GSE89960
Status Public on May 25, 2017
Title An environment-dependent transcriptional network regulates human microglia phenotypes
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Microglia play essential roles in central nervous system (CNS) homeostasis and influence diverse aspects of neuronal function. Although dysregulation of microglia activity is genetically linked to neurodegenerative and behavioral diseases, the transcriptional mechanisms that specify human microglia phenotypes are largely unknown. We report here on the transcriptomes and epigenetic landscapes of human microglia isolated from surgically resected brain tissue, revealing broad similarities but also significant differences with mouse microglia. Many genes associated with risk alleles for neurodegenerative diseases are preferentially or highly expressed in human microglia. The transition of human and mouse microglia from the brain to a tissue culture environment results in rapid and extensive downregulation of genes that are induced in primitive mouse macrophages following migration into the fetal brain. These findings reveal an environment-dependent transcriptional network specifying microglia-specific programs of gene expression and will facilitate efforts to better understand the roles of microglia in human disease.
Overall design We isolated microglia ex vivo from mouse brains using FACS. We also cultured isolated mouse microglia in vitro for varying lengths of time, both with and without TGFB. Various subsets of these cells were assayed with RNA-seq, ATAC-seq, as well as ChIP-seq for the transcription factor PU.1 and the histone marks H3K4me2 and H3K27ac.
Contributor(s) Gosselin D, Skola D, Coufax N, Holtman IR, Schlachetzki JC, O’Connor C, Pasillas MP, Pena M, Adair A, Jaeger B, Gonda DG, Levy ML, Ransohoff RM, Gage FH, Glass CK, Sajit E
Citation(s) 28546318
Submission date Nov 16, 2016
Last update date May 15, 2019
Contact name Dylan Derik Skola
Organization name UCSD
Department Cellular and Molecular Medicine
Lab Dr. Christopher K. Glass
Street address 9500 Gilman Dr.
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (41)
GSM2642931 Mouse_RNA_24hr_Rep1
GSM2642932 Mouse_RNA_24hr_Rep2
GSM2642933 Mouse_RNA_24hr_Rep3
BioProject PRJNA354308
SRA SRP093683

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Supplementary file Size Download File type/resource
GSE89960_mouse_atac_exvivo_vsInput_no_style_factor_region_no_nfr_no_size_200_minDist_200_peaks.bed.gz 1.1 Mb (ftp)(http) BED
GSE89960_mouse_atac_invitro_vsInput_no_style_factor_region_no_nfr_no_size_200_minDist_200_peaks.bed.gz 1.3 Mb (ftp)(http) BED
GSE89960_mouse_h3k27ac_exvivo_vsInput_yes_style_histone_region_yes_nfr_no_size_500_minDist_1000_peaks.bed.gz 347.3 Kb (ftp)(http) BED
GSE89960_mouse_h3k27ac_invitro_vsInput_yes_style_histone_region_yes_nfr_no_size_500_minDist_1000_peaks.bed.gz 432.0 Kb (ftp)(http) BED
GSE89960_mouse_h3k4me2_exvivo_vsInput_yes_style_histone_region_yes_nfr_no_size_500_minDist_1000_peaks.bed.gz 617.0 Kb (ftp)(http) BED
GSE89960_mouse_pu1_exvivo_vsInput_yes_style_factor_region_no_nfr_no_size_200_minDist_200_peaks.bed.gz 970.4 Kb (ftp)(http) BED
GSE89960_mouse_rna_read_counts_sample_ids.csv.gz 759.0 Kb (ftp)(http) CSV
GSE89960_mouse_rna_tpm_trimmed_sample_ids.csv.gz 1.1 Mb (ftp)(http) CSV
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