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Series GSE165578 Query DataSets for GSE165578
Status Public on Aug 11, 2022
Title Microenvironment Impacts the Molecular Architecture and Interactivity of Resident Cells in Marmoset Brain
Organism Callithrix jacchus
Experiment type Expression profiling by high throughput sequencing
Summary We sought to define and compare the diversity of cells across many brain areas, including various white matter (WM) regions, the volume and complexity of which is limited in mouse brain. We employed magnetic resonance (MR) image-guided sampling and snRNA-seq to survey the transcriptome at cellular resolution. Tissue types included WM (frontal, parietal, temporal), corpus callosum (anterior, posterior), optic tract, cerebral cortex (frontal, parietal, temporal, occipital, cingulate), caudate, hippocampus, lateral geniculate nucleus, cerebellum, thalamus, midbrain, pons, and cervical spinal cord. We profiled nuclei from confined regions (cylinders of tissue 2 mm in diameter and 3 mm in height, ~10 μL), which can be consistently located and repeated based on MR images from animal to animal. We analyze and discuss the global landscape of neural cell types across brain regions, comparing compositional differences of subpopulations of glia in GM and WM, modeling intercellular communication in each milieu, and cataloging their contributions to neurological disorders.
Overall design Central nervous system marmoset cell atlas was generated from 2 healthy, 5.5-year-old common marmosets (Callithrix jacchus), one female (CJH01) and one male (CJR02). Most single nucleus libraries (38) were prepared using 10x Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3, 4 libraries were done in v2 chemistry following the manufacture’s protocol (total 42 samples). Briefly, nuclei suspensions were prepared as described above and diluted with resuspension buffer to achieve the desired concentration, and then loaded into Chromium Controller to generate Gelbeads in Emulsion (GEMs). For both cDNA amplification and library sample index PCR, 12 cycles were used. Most libraries were sequenced on Illumina Novaseq S2, but some used Illumina Miseq, Hiseq 2500, or Hiseq 4000, according to manufacturer’s protocol; see Figure S2 and Table S1 for details.
Web link
Contributor(s) Lin J, Kelly HM, Song Y, Kawaguchi R, Geschwind DH, Jacobson S, Reich DS
Citation(s) 36130924
Submission date Jan 26, 2021
Last update date Oct 04, 2022
Contact name Daniel S Reich
Organization name NIH
Department NINDS
Lab Translational Neuroradiology Section (TNS)
Street address 10 Center Drive Bldg 10 Rm 5C103
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
Platforms (3)
GPL18020 Illumina MiSeq (Callithrix jacchus)
GPL26566 Illumina HiSeq 4000 (Callithrix jacchus)
GPL28240 Illumina NovaSeq 6000 (Callithrix jacchus)
Samples (42)
GSM5044267 v2.1.1
GSM5044269 v2.1.3.p
BioProject PRJNA694996
SRA SRP303365

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Supplementary file Size Download File type/resource
GSE165578_CjPCA_dgCMatrix.RData.gz 8.2 Gb (ftp)(http) RDATA 4.3 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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