GEO DataSets

(Submitter supplied) SIRT6 is a well known histone deactylase enzyme. Here, we report the effect of its depletion in nucleus pulposus cells from rattus norvegicus. RNA seq was performed on control and sirt6 depelted cells via lentiviral transfection method. Downstream analysis includes upregulated and downregulated signalling molecules with respect to SIRT6 depletion.

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22396

8 Samples

Download data: CSV

(Submitter supplied) Transcriptional analysis of 24-month-old primary nucleus pulposus (NP) and annulus fibrosus (AF) mouse disc tissues from Sirt6fl/fl and Sirt6cKO mice, which harbor a mutation which constiuitively deletes Sirtuin 6 in aggrecan expressing cells. SIRT6 loss causes intervertebral disc degeneration in mice by dysregulating senescence and SASP status

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL23038

16 Samples

Download data: CEL, CHP

(Submitter supplied) Increasing evidence shows that brain pericytes can acquire multipotency to produce multi-lineage cells following injury. However, pericytes are a heterogenous population and it remains unknown whether there are different potencies from different subsets of pericytes in response to injury. Here, using single-cell RNA-sequencing (scRNA-seq) and immunohistochemistry analysis following ischemic stroke, we showed that NG2+ pericyte subset expressed very strong neural reprogramming potential to produce newborn neurons, while Tbx18+ pericytes displayed strong multipotency to produce endothelial cells, fibroblasts, and microglia but with minimal neural reprogramming potency. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: CSV, LOOM

(Submitter supplied) The tumor microenvironment (TME) comprises all non-tumor elements of cancer and strongly influences disease progression and phenotype. To understand tumor biology and accurately test new therapeutic strategies, representative models should contain both tumor cells and normal cells of the TME. Here we describe and characterize co-culture tumor-derived organoids and cancer-associated fibroblasts (CAFs), a major component of the TME, in matrix-embedded assembloid models of esophageal adenocarcinoma (EAC). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: TXT

(Submitter supplied) Hypoxia inducible factors (HIFs) are critical to the development and homeostasis of the intervertebral disc. While HIF-2α, one of the main HIF-α isoforms is expressed in nucleus pulposus (NP) cells, its functions remain unknown. We used microarrays to explore the transcriptomics of differentially expressed genes between control and HIF-2α cKO NP cells in 6M and 14M mice.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL23038

16 Samples

Download data: CEL

(Submitter supplied) An experimental system was designed to screen for targetable signaling pathways linked to early 3D invasion in molecular subtypes, TP53 and LKB1, of KRAS-driven lung adenocarcinoma (LUAD). Live-cell imaging of human bronchial epithelial cells during 3D invasion was combined with RNA transcriptome profiling shown here.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

18 Samples

Download data: TXT

(Submitter supplied) Hi-C and RNA-seq for a large cohort of pediatric brain tumors including ependymoma (PFA, PFB, Ste, spinal), medulloblastoma (G3, G4, SHH), high grade glioma (H3K27 and H3-WT), pilocytic astrocytoma, and more.

Organism:

Homo sapiens

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL20795

160 Samples

Download data: BED, BEDGRAPH, BEDPE, BROADPEAK, BW, GTF, HIC, MCOOL, RDATA, TDF, TSV, WIG

(Submitter supplied) Some chemotherapy drugs influence the formation of stress granules (SGs), cytoplasmic RNA foci involved in stress response pathways. The exact role of SGs in promoting cell survival or apoptosis needs further clarification. The chemotherapy drug lomustine induces SG formation by activating the eIF2α kinase HRI (EIF2AK1). We performed a DNA microarray transcriptome analysis to identify genes affected by lomustine-induced stress and to explore the role of SGs. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17692

24 Samples

Download data: CEL

(Submitter supplied) The eukaryotic GID/CTLH complex is a highly conserved E3 ubiquitin ligase involved in a broad range of biological processes. However, a role of this complex in host antimicrobial defenses has not been described. We exploited Mycobacterium tuberculosis (Mtb) induced cytotoxicity in macrophages in a FACS based CRISPR genetic screen to identify host determinants of intracellular Mtb growth restriction. more...

Organism:

Mycobacterium tuberculosis; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34461

12 Samples

Download data: TXT

(Submitter supplied) Macrophage function declines with age, however the underlying mechanisms remain poorly understood. Here, we report that MYC and USF1 are key in driving age-related macrophage functional decline in humans, including reduction in phagocytosis and chemotaxis. We show downregulation with age of MYC and USF1 in human monocyte-derived macrophages (MDMs) and crucially, that knockdown of MYC or USF1 in young MDMs modelled the age-related functional changes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

30 Samples

Download data: SF

(Submitter supplied) Transcriptomic analysis of nucleus pulposus (NP) tissues from intervertebral discs of 14- and 24-month-old mice with the conditional postnatal overexpression of HIF-2α. Hypoxia-inducible factors (HIFs) are essential for the homeostasis of the hypoxic tissues, and therefore, increased activity of the transcription factor HIF-2α is shown to contribute to the pathogenesis of mild disc degeneration in the spine. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL23038

16 Samples

Download data: CEL, CHP

(Submitter supplied) Twenty-four patients were randomized to receive Orca-T alone (n=12) or Orca-T plus single-agent GVHD prophylaxis (n=12) to determine if Orca-T alone was non-inferior in preventing acute GVHD.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL24676

52 Samples

Download data: TXT

(Submitter supplied) Tiragolumab, an anti-TIGIT antibody with an active IgG1κ Fc, demonstrated improved outcomes in the phase 2 CITYSCAPE trial (ClinicalTrials.gov: NCT03563716) when combined with atezolizumab (anti-PD-L1) versus atezolizumab alone. However, there remains little consensus on the mechanism(s) of response with this combination. Here we find that a high baseline of intratumoural macrophages and regulatory T cells is associated with better outcomes in patients treated with atezolizumab plus tiragolumab but not with atezolizumab alone. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

46 Samples

Download data: CSV, RDS, TXT

(Submitter supplied) We report both raw and processed scRNA-seq profiling reveals how root tissues adapt to soil conditions and compaction stress

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

14 Samples

Download data: PDF, RDS

(Submitter supplied) Background: Functional enrichment analysis of genome-wide association study (GWAS)-summary statistics has suggested that immune cell-types, and especially CD4+ T-cells, play an important role in asthma pathogenesis. Despite this, CD4+ T-cells are under-represented in asthma transcriptome studies. Objective: To identify differences in gene expression between asthmatics and healthy controls in CD4+ T-cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

43 Samples

Download data: TXT

(Submitter supplied) In plants, plasmodesmata establish cytoplasmic continuity between cells to allow for communication and resource exchange across the cell wall. While plant pathogens use plasmodesmata as a pathway for both molecular and physical invasion, the benefits of molecular invasion (cell-to-cell movement of pathogen effectors) are poorly understood. To establish a methodology for identification and characterization of the cell-to-cell mobility of effectors, we performed a quantitative live imaging-based screen of candidate effectors of the fungal pathogen Colletotrichum higginsianum. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

9 Samples

Download data: TXT

(Submitter supplied) The Phase 3 1L urothelial carcinoma (IMvigor130) trial revealed more favorable effects on overall survival with atezolizumab combined with gemcitabine and cisplatin (GemCis) than with atezolizumab combined with gemcitabine and carboplatin (GemCarbo). This study investigates the immunomodulatory effects of cisplatin vs carboplatin as a potential explanation for these clinical observations. GemCis compared with GemCarbo ± atezolizumab induced transcriptional changes in circulating immune cells, including upregulation of antigen presentation and T-cell activation programs. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL21103

32 Samples

Download data: TXT

(Submitter supplied) Tuberculosis, caused by M.tuberculosis (Mtb), remains an enduring global health challenge, especially given the limited efficacy of current therapeutic interventions. Much of existing research has focused on immune failure as a driver of tuberculosis. However, the crucial role of host macrophage biology in controlling the disease remains underexplored. While we have gained deeper insights into how alveolar macrophages (AMs) interact with Mtb, the precise AM subsets that mediate protection and potentially prevent tuberculosis progression have yet to be identified. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19057 GPL30172

17 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) Tuberculosis, caused by M.tuberculosis (Mtb), remains an enduring global health challenge, especially given the limited efficacy of current therapeutic interventions. Much of existing research has focused on immune failure as a driver of tuberculosis. However, the crucial role of host macrophage biology in controlling the disease remains underexplored. While we have gained deeper insights into how alveolar macrophages (AMs) interact with Mtb, the precise AM subsets that mediate protection and potentially prevent tuberculosis progression have yet to be identified. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

1 Sample

Download data: TBI, TSV

(Submitter supplied) This project uses the massively parallel reporter assay, mSTARR-seq (Lea et al., 2018) to simultaneously test for both enhancer-like activity and DNA methylation-dependent enhancer activity across nearly the entire human genome. We assessed enhancer activity at almost all CpG sites profiled either on the commonly used Illumina Infinium MethylationEPIC array or via reduced representation bisulfite sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data: TXT