GEO DataSets

(Submitter supplied) Human CD8 EGFR CART cells during expansion and repeated hypoxic coculture were collected at different time points and subject to RNA-seq to identify key players in T cell differentiation and hypoxia-induced exhaustion. The RNA-seq data together with other functional analysis identified P4HA1 as an important enzyme that regulates T cell early differentiation and terminal exhaustion. To investigate the mechanism, P4HA1 inhibitor DPCA was used to treat the human CD8 cells during early expansion and repeated coculture and the cells were harvested for RNA-seq analysis.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

24 Samples

Download data: CSV

(Submitter supplied) Somatic variation contributes to biological heterogeneity by modulating the cellular proclivity to differentiate, expand, adapt, or die. While large-scale sequencing efforts have revealed the foundational role of somatic variants to drive human tumor evolution, our understanding of the contribution of somatic variation to modulate cellular fitness in non-malignant contexts remains understudied. Here, we identify a somatic synonymous variant (m.7076A>G) in the mitochondrial DNA (mtDNA) encoded cytochrome c-oxidase subunit 1 gene (COX1), which was present at homoplasmy in 47% of immune cells from a healthy donor. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL21697

12 Samples

Download data: TSV

(Submitter supplied) Somatic variation contributes to biological heterogeneity by modulating the cellular proclivity to differentiate, expand, adapt, or die. While large-scale sequencing efforts have revealed the foundational role of somatic variants to drive human tumor evolution, our understanding of the contribution of somatic variation to modulate cellular fitness in non-malignant contexts remains understudied. Here, we identify a somatic synonymous variant (m.7076A>G) in the mitochondrial DNA (mtDNA) encoded cytochrome c-oxidase subunit 1 gene (COX1), which was present at homoplasmy in 47% of immune cells from a healthy donor. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL24676

2 Samples

Download data: H5, MTX, TXT

(Submitter supplied) Somatic variation contributes to biological heterogeneity by modulating the cellular proclivity to differentiate, expand, adapt, or die. While large-scale sequencing efforts have revealed the foundational role of somatic variants to drive human tumor evolution, our understanding of the contribution of somatic variation to modulate cellular fitness in non-malignant contexts remains understudied. Here, we identify a somatic synonymous variant (m.7076A>G) in the mitochondrial DNA (mtDNA) encoded cytochrome c-oxidase subunit 1 gene (COX1), which was present at homoplasmy in 47% of immune cells from a healthy donor. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

2 Samples

Download data: CSV, H5, TSV

(Submitter supplied) Somatic variation contributes to biological heterogeneity by modulating the cellular proclivity to differentiate, expand, adapt, or die. While large-scale sequencing efforts have revealed the foundational role of somatic variants to drive human tumor evolution, our understanding of the contribution of somatic variation to modulate cellular fitness in non-malignant contexts remains understudied. Here, we identify a somatic synonymous variant (m.7076A>G) in the mitochondrial DNA (mtDNA) encoded cytochrome c-oxidase subunit 1 gene (COX1), which was present at homoplasmy in 47% of immune cells from a healthy donor. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

5 Samples

Download data: CSV

(Submitter supplied) The ultimate goal of immunometabolism is to modulate metabolic pathways to enhance immunity. Here, we investigate the potential of an alternative oxidase (AOX) to counteract cytochrome c oxidase (COX) deficiency in T cells. COX is vital for oxidative phosphorylation (OXPHOS), and its deficiency leads to redox imbalances, impaired metabolism, reactive oxygen species (ROS), and apoptosis, resulting in T cell immunodeficiency. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

24 Samples

Download data: TXT

(Submitter supplied) Interleukin-4 activated human macrophages (M(IL4) promote epithelial wound healing and exert an anti-colitic effect. Blood monocyte-derived M(IL4)s from healthy donors and individuals with Crohn’s disease had increased mRNA expression of the calcitonin gene-related peptide (CGRP) receptor chain, RAMP1, suggesting neural modulation of the M(IL4)s function. Thus, human (MIL4)s were treated with CGRP and the cells' phagocytic, epithelial wound repair and anti-colitic functions were assessed. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: TXT

(Submitter supplied) Our RNAseq results showed that P2RY6 induced the expression of Ptgs1 and Ptgs2 in MC38 cells. To confirm whether P2RY6 increases the opening of cis-regulatory elements to promote Ptgs1/2 transcription, we performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to determain the chromatin accessibility across the genome in MC38 cells with or without P2RY6 expression.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: BW

(Submitter supplied) The importance of parental diet in relation to eventual offspring health is increasing in prominence due to the increased frequency of reproductive age adults consuming poor diets. Whilst maternal health and offspring outcome have been studied in some detail, the paternal impacts are not as well understood. A father’s poor nutritional status has been shown to have negative consequences on fetal growth and development and ultimately impact the long-term adult health of the offspring. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

25 Samples

Download data: XLSX

(Submitter supplied) Mitochondrial oxidative phosphorylation (OXPHOS) fuels cellular ATP demands. OXPHOS defects lead to severe human disorders with unexplained tissue specific pathologies. Mitochondrial gene expression is essential for OXPHOS biogenesis since core subunits of the complexes are mitochondrial-encoded. COX14 is required for translation of COX1, the central mitochondrial-encoded subunit of complex IV. Here we describe a COX14 mutant mouse corresponding to a patient with complex IV deficiency. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

8 Samples

Download data: CSV

(Submitter supplied) Tissue regeneration after injury involves the dedifferentiation of somatic cells, a natural adaptive reprogramming that leads to the emergence of injury-responsive cells with fetal-like characteristics. However, there is no direct evidence that adaptive reprogramming involves a shared molecular mechanism with direct cellular reprogramming. Here, we induced dedifferentiation of intestinal epithelial cells using OSKM (Oct4, Sox2, Klf4, and c-Myc) in vivo. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

4 Samples

Download data: TXT

(Submitter supplied) Tissue regeneration after injury involves the dedifferentiation of somatic cells, a natural adaptive reprogramming that leads to the emergence of injury-responsive cells with fetal-like characteristics. However, there is no direct evidence that adaptive reprogramming involves a shared molecular mechanism with direct cellular reprogramming. Here, we induced dedifferentiation of intestinal epithelial cells using OSKM (Oct4, Sox2, Klf4, and c-Myc) in vivo. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

8 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL19057 GPL28457

20 Samples

Download data: H5

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

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL24676 GPL24106

48 Samples

Download data: TSV, TXT

(Submitter supplied) Mitochondrial oxidative phosphorylation (OXPHOS) complexes are assembled from proteins encoded by both nuclear and mitochondrial DNA. These dual-origin enzymes pose a complex gene regulatory challenge for cells requiring coordinated gene expression across organelles. To identify genes involved in dual-origin protein complex synthesis, we performed FACS-based genome-wide screens analyzing mutant cells with unbalanced levels of mitochondrial- and nuclear-encoded subunits of Complex IV. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

14 Samples

Download data: CSV

(Submitter supplied) Single-cell RNA sequencing was used to show the heterogeneity of conventional dendritic cells in the immunigenic murine melanoma BRAFV600E Ptgs1/Ptgs2-/-. Our analysis shows that on day 6 of tumor growth, 3 distinct populations of cDC1 and 2 distinct populations of cDC2 can be found in the tumor microenvironment. The differentially expressed genes of these populations indicate a functional heterogeneity.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

1 Sample

Download data: CSV, FASTA, XLSX

(Submitter supplied) The arachidonic acid pathway participates in immunosuppression in various types of cancer. Our previous observation detailed that microsomal prostaglandin E2 synthase 1 (mPGES-1), an enzyme downstream of cyclooxygenase 2 (COX-2), limited antitumor immunity in melanoma; in addition, genetic depletion of mPGES-1 specifically enhanced immune checkpoint blockade therapy. The present study set out to distinguish the roles of mPGES-1 from those of COX-2 in tumor immunity and determine the potential of mPGES-1 inhibitors for reinforcing immunotherapy in melanoma. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

12 Samples

Download data: TXT

(Submitter supplied) RNA sequencing was used to characterize in situ tumor infiltrating conventional type 1 dendritic cells (cDC1) in BRAFV600E melanoma tumors transplanted into C57BL/6 wildtype mice. Our analysis shows PGE2-dependent differences in the gene expression profile of intratumoral cDC1.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

23 Samples

Download data: TXT

(Submitter supplied) RNA sequencing was used to characterize PGE2-mediated changes in the gene expression profile of conventional type 1 dendritic cells (cDC1). Our analysis shows that treatment of cDC1 with PGE2 or conditioned medium from PGE2-producing tumors induces transcriptional changes in resting cDC1. cDC1 activated with a TLR3 ligand after PGE2 pre-treatment show alterations in the expression of activation induced genes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

52 Samples

Download data: TXT

(Submitter supplied) Abstract Objective: Osteoarthritis (OA) is accompanied by severe and debilitating pain that current analgesics are unable to fully alleviate. A multitude of signaling molecules, pathways, and cells have been identified as regulators of OA pain. Fatty acid binding protein 5 (FABP5) regulates pain in other disease states and we hypothesized that it is involved in the regulation of OA pain. Design: This was a combined clinical and pre-clinical study. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25029

16 Samples

Download data: TXT