GPL27943[Accession] - GEO DataSets

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Select item 2001830521.

Single-cell RNA-sequencing analysis for the molecular taxonomy of primate Anterior cingulate cortex (ACC) and Retro splenial cortex (RSC), as well as rodents

(Submitter supplied) We thus isolated Anterior cingulate cortex (ACC) and Retro splenial cortex (RSC) from rhesus macaques and mice and performed single-cell RNA-sequencing analysis.The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V2 Reagent Kits (10X Genomics, Pleasanton, USA).

Organism:: Mus musculus; Macaca mulatta

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL27943 GPL24247
11 Samples

Download data: MTX, TSV

Series

Accession:: GSE183052

ID:: 200183052

SRA Run Selector

Select item 2002665762.

Distinct SIV-specific lymphoid tissue CD8 T cells exhibit simultaneous effector and stem-like profiles and associate with limited SIV persistence

(Submitter supplied) HIV cure efforts are increasingly focused on harnessing CD8 T cell functions; however, a deeper understanding of CD8 T cells promoting HIV control is necessary to properly inform therapeutic approaches. Here, we identified a novel TOX-expressing CD8 T cell population associated with control of SIV infection in lymphoid tissue of rhesus macaques defined as an antigen-responsive TCF1+ CD39+ subset expressing high levels of TOX and inhibitory receptors but lower levels of canonical cytolytic molecules such as granzyme B, granzyme A, and perforin. more...

Organism:: Macaca mulatta

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27943
5 Samples

Download data: H5

Series

Accession:: GSE266576

ID:: 200266576

Select item 2002676593.

Optimizing RNA Extraction Methods for High Throughput Transcriptome Sequencing of Fresh Frozen and Formalin-Fixed Paraffin-Embedded Cardiac Tissues Specimens

(Submitter supplied) In this study, the efficiency of four RNA extraction methods was compared on 23 FFPE cardiac tissue specimens. The Qiagen AllPrep DNA/RNA FFPE kit (Method QP), Qiagen AllPrep DNA/RNA FFPE kit, with protocol modification on the ethanol wash step after deparaffinization (Method QE), CELLDATA RNAstorm 2.0 FFPE RNA Extraction kit (Method BP) and CELLDATA RNAstorm 2.0 FFPE RNA Extraction Kit with protocol modifications on the lysis step (Method BL). more...

Organism:: Macaca mulatta

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27943
16 Samples

Download data: XLSX

Series

Accession:: GSE267659

ID:: 200267659

Select item 2002136934.

Comparative 3D genomic architectures elucidate the function of the adaptive human-specific inversions in human brain evolution

(Submitter supplied) Structural variation (SV) is a class of genetic variants involving long stretches of DNA and provides substantial innovations for adaptation and evolution. Investigation of SV profiles and turnover in nonhuman primates can help answer fundamental questions, such as what makes us uniquely human. Here, we present the high-resolution comparative 3D genome organizations of prefrontal cortex (PFC) of adult human and rhesus macaque. more...

Organism:: Macaca mulatta; Homo sapiens

Type:: Other

Platforms:: GPL24676 GPL27943
2 Samples

Download data: BED, BEDPE

Series

Accession:: GSE213693

ID:: 200213693

Select item 2001747425.

m6A-Seq analysis for the methylated RNA of primate prefrontal cortex after sevoflurane exposure

(Submitter supplied) We thus isolated prefrontal cotex from rhesus macaques and performed m6A-Seq analysis.MeRIP libraries using eluted RNA were constructed using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian User Manual according to the manufacturer’s instructions.

Organism:: Macaca mulatta

Type:: Other

Platform:: GPL27943
22 Samples

Download data: TXT

Series

Accession:: GSE174742

ID:: 200174742

SRA Run Selector

Select item 2002646576.

SIV infection and ARV treatment reshape the transcriptional and epigenetic profile of naïve and memory T cells in vivo (RNA-Seq)

(Submitter supplied) Here we use RNAseq and ATACseq to study the transcriptomics and epigenetic landscape of longitudinally sampled naïve and memory CD4+ and CD8+ T cells in two species of non-human primates prior to SIV infection, during chronic SIV infection, and after administration of ARVs. We find that SIV infection leads to significant alteration to the transcriptomic profile of all T cell subsets that are only partially reversed by administration of ARVs. more...

Organism:: Macaca nemestrina; Macaca mulatta

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL27943 GPL33261
116 Samples

Download data: TXT

Series

Accession:: GSE264657

ID:: 200264657

Select item 2002646567.

SIV infection and ARV treatment reshape the transcriptional and epigenetic profile of naïve and memory T cells in vivo (ATAC-Seq)

Organism:: Macaca nemestrina; Macaca mulatta

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL33261 GPL27943
120 Samples

Download data: BW, NARROWPEAK

Series

Accession:: GSE264656

ID:: 200264656

Select item 2002538358.

Immunotyping of microglia and macrophages in the CNS during acute SIV infection: a single-cell study of rhesus macaque brains

(Submitter supplied) Human immunodeficiency virus (HIV) is widely recognized for its striking impact on the immune system. Even though HIV is primarily known for the impairment of the peripheral CD4 T cells, its influence on the central nervous system (CNS) also cannot be neglected. The main immune constituents in the brain, microglia and macrophages, are the target for HIV in the brain, as well as for the simian immunodeficiency virus (SIV) in nonhuman primates. more...

Organism:: Macaca mulatta

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL27943 GPL29319
20 Samples

Download data: H5

Series

Accession:: GSE253835

ID:: 200253835

PubMed Full text in PMC Similar studies

Select item 2002633999.

Natural killer cell receptor expressing B cells: a distinct but rare subset of innate immune cells in rhesus macaques

(Submitter supplied) Natural killer-like B (NKB) cells are unique innate immune cells that express both natural killer (NK) and B cell markers. They act as first responders by secreting IL-18 upon infection, thus inducing the critical cascade of innate and adaptive immune cell infiltration and activation. However, limited research exists on the role of NKB cells in homeostasis, and infection in primates. Therefore, we investigated the signaling and trafficking proteome, in situ localization and transcriptome of NKB cells in comparison to conventionally defined NK and B cells. more...

Organism:: Macaca mulatta

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27943
314 Samples

Download data: TXT

Series

Accession:: GSE263399

ID:: 200263399

Select item 20024455710.

Chronic alcohol drinking modulates synchrony between midbrain gene transcription and long-lasting changes in dopamine terminal and opioid function in macaques

(Submitter supplied) Alcohol use disorder is marked by disrupted behavioral and emotional states which can persist into abstinence. The enduring synaptic alterations that remain despite the absence of alcohol are of interest for interventions to prevent relapse. 28 male rhesus macaques underwent over 20 months of alcohol drinking interspersed with three 30-day forced abstinence periods. After the last abstinence period, we paired ex vivo voltammetry in nucleus accumbens slices with RNA-sequencing of the ventral tegmental area. more...

Organism:: Macaca mulatta

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27943
28 Samples

Download data: CSV, XLSX

Series

Accession:: GSE244557

ID:: 200244557

PubMed Full text in PMC Similar studies

Select item 20024113111.

Dysregulation of Neuroprotective Lipoxin Pathway in Astrocytes in Response to Cytokines and Ocular Hypertension

(Submitter supplied) Glaucoma leads to vision loss due to retinal ganglion cell death. Astrocyte reactivity contributes to neurodegeneration. Our recent study found that lipoxin B4 (LXB4), produced by retinal astrocytes, has direct neuroprotective actions on retinal ganglion cells. In this study, we aimed to investigate how the autacoid LXB4 influences astrocyte reactivity in the retina under inflammatory cytokine-induced activation and ocular hypertension conditions. more...

Organism:: Macaca mulatta

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27943
2 Samples

Download data: CSV

Series

Accession:: GSE241131

ID:: 200241131

PubMed Full text in PMC Similar studies

Select item 20024541912.

B cell directed CAR-T cell therapy results in activation of CD8+ cytotoxic CAR-negative bystander T cells in both non-human primates and patients

(Submitter supplied) There is growing appreciation for the emergence of CARneg bystander T cells after CAR-T cell infusion. However, their phenotypic and transcriptomic hallmarks and mechanisms of activation remain uncertain. We performed single-cell RNA-Seq (scRNA-Seq) on non-human primate (NHP) and patient-derived T cells to interrogate CARneg T cells following B cell targeted CAR-T cell therapy. In a NHP model, we observed a distinct population of activated CD8+ CARneg T cells emerging during CAR-T cell expansion. more...

Organism:: Macaca mulatta

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27943
35 Samples

Download data: HDF5, PT

Series

Accession:: GSE245419

ID:: 200245419

Select item 20024990713.

(Submitter supplied) The hippocampus is especially susceptible to age-associated neuronal pathologies, and there is concern that the age-associated rise in cortisol secretion from the adrenal gland may contribute to their etiology. Furthermore, because 11β-hydroxysteroid dehydrogenase type 1 (HSD11B1) catalyzes the reduction of cortisone to the active hormone cortisol, it is plausible that an increase in the expression of this enzyme enhances the deleterious impact of cortisol in the hippocampus and contributes to the neuronal pathologies that underlie cognitive decline in the elderly. more...

Organism:: Macaca mulatta

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27943
28 Samples

Download data: CSV

Series

Accession:: GSE249907

ID:: 200249907

PubMed Full text in PMC Similar studies

Select item 20026196914.

Spatial transcriptomics of the Rhesus Macaque Hippocampus during homeostasis and chronic SIV CL757 infection

(Submitter supplied) We performed spatial transcriptomics using Nanostring's DSP platform on Rhesus Macaque Hippocampal Brain sections obtained from one uninfected control and one chronically infected with SIVCL757. Our goals were to (1) determine which differentially expressed genes (DGEs) could be attributed to SIV infection in the rhesus hippocampus, (2) determine if spatial transcriptomics could serve as a tool to identify leukocyte infiltrates in the SIV infected brain and (3) examine localization of leukocytes at homeostatasis and chronic SIV infection

Organism:: Macaca mulatta

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27943
48 Samples

Download data: DCC

Series

Accession:: GSE261969

ID:: 200261969

Select item 20026196815.

Chromatin and gene expression profile at single nuclei level of CD45+ leukocytes from the rhesus brain parenchyma

(Submitter supplied) We used Chromium Single Cell Multiome ATAC + Gene Expression to analyze CD45+ leukocytes in the rhesus macaque brain during homeostasis and chronic SIV infection

Organism:: Macaca mulatta

Type:: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL27943
8 Samples

Download data: H5, TSV

Series

Accession:: GSE261968

ID:: 200261968

Select item 20023396216.

Single-cell analysis reveals transcriptional dynamics in primary parathyroid tissue

(Submitter supplied) Studies on human parathyroid tissue are often limited to adenomatous tissue due to difficulty obtaining healthy tissue. We obtained nonhuman primate parathyroids to provide a suitable alternative for sequencing analysis that would bear the closest semblance to human organs as possible. We analyzed four M. mulatta normal parathyroid specimens to that show a continuous trajectory of cell states comprising the normal adult parathyroid. more...

Organism:: Macaca mulatta; Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL27943 GPL24676
8 Samples

Download data: MTX, TSV

Series

Accession:: GSE233962

ID:: 200233962

Select item 20026104717.

Correlation of antigen expression with epigenetic modifications after rAAV delivery of a hyperactive human Factor IX variant in mice and rhesus macaques

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:: Mus musculus; Macaca mulatta

Type:: Genome binding/occupancy profiling by high throughput sequencing; Other

4 related Platforms
64 Samples

Download data: BEDGRAPH

Series

Accession:: GSE261047

ID:: 200261047

Select item 20026104618.

Correlation of antigen expression with epigenetic modifications after rAAV delivery of a hyperactive human Factor IX variant in mice and rhesus macaques (Tn5 NHP)

(Submitter supplied) We investigated long-term human coagulation Factor IX expression of a novel variant when delivered into mice and rhesus macaques and compare transduction efficiencies using two different AAV capsids. In hemophilic mice injected with KP1-packaged rAAV expressing the hyperactive FIX variant specific activity plasma levels were 10-fold or 2-fold enhanced when compared to wild-type or Padua huFIX injected mice, respectively. more...