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Series GSE126836 Query DataSets for GSE126836
Status Public on Feb 21, 2019
Title Single-cell multi-omic integration compares and contrasts features of brain cell identity
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary To flexibly model single-cell datasets, we developed LIGER, an algorithm and software package that delineates shared and dataset-specific features of cell identity. We applied it to four diverse and challenging analyses of human and mouse brain cells, the first two of which include newly generated single-cell transcriptome datasets for mouse and human regions. First, we determined region-specific and sexually dimorphic gene expression in the mouse bed nucleus of the stria terminalis (BNST). Second, we analyzed expression in the human substantia nigra (SN), integrating cell types across donors, and relating cell types to those in the mouse (using mouse SN data from Saunders et al., 2018 (GEO: GSE116470)). The main cell types identified include neurons, astrocytes, microglia, oligodendrocytes, polydendrocytes, and endothelial cells. Third, we jointly leveraged in situ and single-cell expression data to spatially locate fine subtypes of cells present in the mouse frontal cortex. Finally, we integrated mouse cortical single-cell RNA-seq and DNA methylation profiles, revealing mechanisms of cell-type-specific gene regulation. Integrative analyses using LIGER promise to accelerate investigations of cell-type definition, gene regulation, and disease states.
Overall design Single nuclei were extracted and isolated from 1mm biopsy punches from the BNST of 15 mouse brains (8 male and 7 female replicates), and sequenced using the 10X Chromium system (V3). In total, 204,737 BNST nuclei were recovered. Single nuclei were extracted and isolated from manually dissected samples of the SN of seven de-identified postmortem human donors, and sequenced using the 10X chromium system (V2). In total, 44,274 SN nuclei were recovered.
Contributor(s) Welch J, Kozareva V, Ferreira A, Vanderburg C, Martin C, Macosko E
Citation(s) 31178122
Submission date Feb 20, 2019
Last update date Dec 24, 2019
Contact name Evan Macosko
Organization name Broad Institute
Street address 75 Ames St, Broad Institute
City Cambridge
State/province Ma
ZIP/Postal code 02142
Country USA
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (50)
GSM3615014 BNST_Female_1a
GSM3615015 BNST_Female_2a
GSM3615016 BNST_Female_3a
BioProject PRJNA523430
SRA SRP186408

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Supplementary file Size Download File type/resource
GSE126836_BNST_only_Fem_barcodes.csv.gz 190.7 Kb (ftp)(http) CSV
GSE126836_BNST_only_Fem_genes.csv.gz 96.1 Kb (ftp)(http) CSV
GSE126836_BNST_only_Fem_matrix.mtx.gz 350.7 Mb (ftp)(http) MTX
GSE126836_BNST_only_Mal_barcodes.csv.gz 174.5 Kb (ftp)(http) CSV
GSE126836_BNST_only_Mal_genes.csv.gz 96.1 Kb (ftp)(http) CSV
GSE126836_BNST_only_Mal_matrix.mtx.gz 335.2 Mb (ftp)(http) MTX
GSE126836_BNST_region_neur_Fem_barcodes.csv.gz 254.6 Kb (ftp)(http) CSV
GSE126836_BNST_region_neur_Fem_genes.csv.gz 97.0 Kb (ftp)(http) CSV
GSE126836_BNST_region_neur_Fem_matrix.mtx.gz 485.2 Mb (ftp)(http) MTX
GSE126836_BNST_region_neur_Mal_barcodes.csv.gz 251.8 Kb (ftp)(http) CSV
GSE126836_BNST_region_neur_Mal_genes.csv.gz 97.0 Kb (ftp)(http) CSV
GSE126836_BNST_region_neur_Mal_matrix.mtx.gz 501.0 Mb (ftp)(http) MTX
GSE126836_SN_MD5534_barcodes.csv.gz 53.7 Kb (ftp)(http) CSV
GSE126836_SN_MD5534_genes.csv.gz 83.9 Kb (ftp)(http) CSV
GSE126836_SN_MD5534_matrix.mtx.gz 34.0 Mb (ftp)(http) MTX
GSE126836_SN_MD5828_barcodes.csv.gz 8.8 Kb (ftp)(http) CSV
GSE126836_SN_MD5828_genes.csv.gz 83.9 Kb (ftp)(http) CSV
GSE126836_SN_MD5828_matrix.mtx.gz 5.3 Mb (ftp)(http) MTX
GSE126836_SN_MD5840_barcodes.csv.gz 25.6 Kb (ftp)(http) CSV
GSE126836_SN_MD5840_genes.csv.gz 83.9 Kb (ftp)(http) CSV
GSE126836_SN_MD5840_matrix.mtx.gz 18.0 Mb (ftp)(http) MTX
GSE126836_SN_MD5862_barcodes.csv.gz 10.2 Kb (ftp)(http) CSV
GSE126836_SN_MD5862_genes.csv.gz 83.9 Kb (ftp)(http) CSV
GSE126836_SN_MD5862_matrix.mtx.gz 6.0 Mb (ftp)(http) MTX
GSE126836_SN_MD5893_barcodes.csv.gz 28.5 Kb (ftp)(http) CSV
GSE126836_SN_MD5893_genes.csv.gz 83.9 Kb (ftp)(http) CSV
GSE126836_SN_MD5893_matrix.mtx.gz 18.2 Mb (ftp)(http) MTX
GSE126836_SN_MD6060_barcodes.csv.gz 37.2 Kb (ftp)(http) CSV
GSE126836_SN_MD6060_genes.csv.gz 83.9 Kb (ftp)(http) CSV
GSE126836_SN_MD6060_matrix.mtx.gz 31.2 Mb (ftp)(http) MTX
GSE126836_SN_MD6063_barcodes.csv.gz 72.1 Kb (ftp)(http) CSV
GSE126836_SN_MD6063_genes.csv.gz 83.9 Kb (ftp)(http) CSV
GSE126836_SN_MD6063_matrix.mtx.gz 65.6 Mb (ftp)(http) MTX
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