GEO DataSets

(Submitter supplied) EM-Seq of DNA derived from freshly sorted AT2 cells from aged (24-30 months old) and young (3-4 months old) C57BL6/J mice

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24247

44 Samples

Download data: BW, RDS

(Submitter supplied) Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based, transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hindered by the massive density of bacterial mRNA. To overcome this challenge, we combine 1000-fold volumetric expansion with multiplexed error robust fluorescence in situ hybridization (MERFISH) to create bacterial-MERFISH, a method enabling high-throughput, spatially resolved profiling of thousands of operons within individual bacteria. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21117 GPL26592

3 Samples

Download data: FASTA, SF

(Submitter supplied) Although mutations in human patatin-like phospholipase PNPLA6 are associated with hereditary retinal degenerative diseases, its mechanistic action in the retina is poorly understood. Here, we uncover the molecular mechanism by which PNPLA6 dysfunction disturbs retinal homeostasis and visual function. PNPLA6, by acting as a phospholipase B, regulates choline mobilization from phosphatidylcholine and subsequent choline turnover for phosphatidylcholine regeneration in retinal pigment epithelial (RPE) cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10333

2 Samples

Download data: TXT

(Submitter supplied) Although mutations in human patatin-like phospholipase PNPLA6 are associated with hereditary retinal degenerative diseases, its mechanistic action in the retina is poorly understood. Here, we uncover the molecular mechanism by which PNPLA6 dysfunction disturbs retinal homeostasis and visual function. PNPLA6, by acting as a phospholipase B, regulates choline mobilization from phosphatidylcholine and subsequent choline turnover for phosphatidylcholine regeneration in retinal pigment epithelial (RPE) cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10332

4 Samples

Download data: TXT

(Submitter supplied) Interaction of mast cells (MCs) with fibroblasts is essential for MC maturation within tissue microenvironments, although the underlying mechanism is incompletely understood. Through a phenotypic screening of >30 mouse lines deficient in lipid-related genes, we found that deletion of the lysophosphatidic acid (LPA) receptor LPA1, like that of the phospholipase PLA2G3, the prostaglandin D2 (PGD2) synthase L-PGDS, or the PGD2 receptor DP1, impairs MC maturation and thereby anaphylaxis. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10333

4 Samples

Download data: TXT

(Submitter supplied) Interaction of mast cells (MCs) with fibroblasts is essential for MC maturation within tissue microenvironments, although the underlying mechanism is incompletely understood. Through a phenotypic screening of >30 mouse lines deficient in lipid-related genes, we found that deletion of the lysophosphatidic acid (LPA) receptor LPA1, like that of the phospholipase PLA2G3, the prostaglandin D2 (PGD2) synthase L-PGDS, or the PGD2 receptor DP1, impairs MC maturation and thereby anaphylaxis. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10333

6 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; Other

Platforms:

GPL19057 GPL30172

20 Samples

Download data: MTX, TSV, ZIP

(Submitter supplied) We monitored lung fibrosis formation and resolution in young and old mice by generating a series of spatial transcriptomics datasets using the 10x Genomics Visium platform

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL30172

8 Samples

Download data: ZIP

(Submitter supplied) Immune self-tolerance is the ability of a host’s immune system to recognize and avoid triggering immune responses against self-tissue. This allows the host to avoid self-directed immune damage, while still responding appropriately to pathogen infection. A breakdown of self-tolerance can lead to an autoimmune state in which immune cells target healthy self-tissue, leading to inflammation and tissue damage. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25244

9 Samples

Download data: TXT

(Submitter supplied) CTCF, a highly studied transcription factor, is essential for chromatin interaction maintenance. Several independent studies have reported that CTCF interacts with RNAs in vitro and in cells. Yet continuous debates about the authenticity of the RNA-binding affinity of CTCF and its biological role remain in large part due to limited research techniques available, such as CLIP-seq. Here, we investigated the role RNA plays on CTCF’s transcription factor function through its chromatin occupancy. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

14 Samples

Download data: BW

(Submitter supplied) Human gut Bacteroides species encode numerous (eight or more) tightly regulated capsular polysaccharides (CPS). Specialized paralogs of the universal transcription elongation factor NusG, called UpxY (Y), and an anti-Y UpxZ (Z) are encoded by the first two genes of each CPS operon. The Y-Z regulators combine with promoter inversions to limit CPS transcription to a single operon in most cells. Y enhances transcript elongation whereas Z inhibits noncognate Ys. more...

Organism:

Bacteroides fragilis NCTC 9343

Type:

Other

Platform:

GPL35091

1 Sample

Download data: TXT

(Submitter supplied) mRNA profiles of primary mouse chondrocytes exposed to senescence stress (bleomycin, doxorubicin) or acute inflammation (interleukin-1 beta) were generated by mRNA sequencing. This study provides transcriptome landscape of senescent chondrocytes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

16 Samples

Download data: TAB

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL23159 GPL24247 GPL24676

74 Samples

Download data: CEL, TSV

(Submitter supplied) Small cell lung cancer (SCLC) patients experience rapid disease progression despite frequently achieving a complete response to first-line therapy. Maintenance treatments, aiming at controlling residual tumor cells, generally fail due to cross-resistance, inability to target tumor vulnerabilities, or dose-limiting side effects. Here, we show that SCLC cells, like their cell-of-origin, pulmonary neuroendocrine cells (PNECs), exhibit notably low activity in pathways protecting against reactive oxygen species (ROS). more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL24676

50 Samples

Download data: TSV

(Submitter supplied) There is an urgent need for agents that promote health and regeneration of cells and tissues, specifically to treat diseases of the aging nervous system. Age-associated nervous system degeneration and various diseases are driven by many different biochemical stresses, often making it difficult to target any one disease cause. Our laboratory has previously identified DNA aptamers with apparent regenerative properties in murine models of multiple sclerosis by selecting aptamers that bind oligodendrocyte membrane preparations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15520

24 Samples

Download data: SF

(Submitter supplied) Pediatric mesenchymal stem cells (pMSCs) within the bone marrow (BM) niche play a crucial role in regulating pediatric acute myeloid leukemia (pAML) survival and therapy resistance. In this study, we isolated pMSCs from pAML bone marrow samples and characterized their phenotype and differentiation potential. We performed coculture experiments with pAML cells in both autologous and allogenic settings, with and without direct contact. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

12 Samples

Download data: TXT

(Submitter supplied) mRNA profiles of primary mouse chondrocytes treated with bleomycin, followed by DMSO or ST045849 were generated by mRNA sequencing. This study provides insights into the role of O-GlcNAcylation in chondrocytes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

9 Samples

Download data: TAB

(Submitter supplied) We performed transcriptome sequencing analysis on LCSCs with different metastatic abilities. KEGG enrichment showed that genes upregulated during LCSC3 metastasis were related to cell membrane pathways. qPCR and flow cytometry confirmed that FASN expression was significantly upregulated during LCSCs metastasis. ICAM1 affects EMT, invadopodia formation, migration and invasion ability of LCSCs. ICAM1 plays a key role in the process of liver metastasis and the development of hepatocellular carcinoma in mice. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: TXT

(Submitter supplied) The human silencing hub (HUSH) complex is a transcription-dependent, epigenetic repressor complex that provides a genome-wide immunosurveillance system for the recognition and silencing of newly-integrated retroelements. The core HUSH complex of TASOR, MPP8 and Periphilin, represses these retroelements through SETDB1-mediated H3K9me3 deposition and MORC2-dependent chromatin compaction. HUSH-dependent silencing is RNA-mediated, yet no HUSH components encode any RNA-binding domain. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL22790

14 Samples

Download data: BIGWIG

(Submitter supplied) We performed transcriptome sequencing analysis on LCSCs with different metastatic abilities. KEGG enrichment showed that genes upregulated during LCSC3 metastasis were related to cell membrane pathways. qPCR and flow cytometry confirmed that FASN expression was significantly upregulated during LCSCs metastasis. ICAM1 affects EMT, invadopodia formation, migration and invasion ability of LCSCs. ICAM1 plays a key role in the process of liver metastasis and the development of hepatocellular carcinoma in mice. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: TXT