GEO DataSets

(Submitter supplied) The cross-species molecular heterogeneity from mice to patients poses grand challenges for translational research endeavors. A high-fat diet (HFD) model and a genetic model (BTBR ob/ob) at different stand points were used to generate cell atlases of diabetic and obese mise. We identified a previously unrecognized, expanding Trem2-High macrophage population in kidneys of HFD mice that modeled human TREM2-high macrophages in obese patients. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

41 Samples

Download data: H5

(Submitter supplied) We sought to characterize cellular composition across the cardiovascular system of the healthy Wistar rat, an important model in preclinical cardiovascular research. We performed snRNA-seq in 78 samples in 10 distinct regions including the four chambers of the heart, ventricular septum, sinoatrial node, atrioventricular node, aorta, pulmonary artery, and pulmonary veins, which produced 505,835 nuclei. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25029

78 Samples

Download data: GTF, H5, XLSX

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL21273 GPL24247

25 Samples

Download data: CSV, H5AD, MTX, TAR, TSV, TXT

(Submitter supplied) While advances in single cell genomics have helped to chart the cellular components of tumor ecosystems, it has been more challenging to characterize their specific spatial organization and functional interactions. Here, we combine single cell RNA-seq, spatial transcriptomics by Slide-seq, and in situ multiplex RNA analysis, to create a detailed spatial map of healthy and dysplastic colon cellular ecosystems and their association with disease progression. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

2 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) While advances in single cell genomics have helped to chart the cellular components of tumor ecosystems, it has been more challenging to characterize their specific spatial organization and functional interactions. Here, we combine single cell RNA-seq, spatial transcriptomics by Slide-seq, and in situ multiplex RNA analysis, to create a detailed spatial map of healthy and dysplastic colon cellular ecosystems and their association with disease progression. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

4 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) While advances in single cell genomics have helped to chart the cellular components of tumor ecosystems, it has been more challenging to characterize their specific spatial organization and functional interactions. Here, we combine single cell RNA-seq, spatial transcriptomics by Slide-seq, and in situ multiplex RNA analysis, to create a detailed spatial map of healthy and dysplastic colon cellular ecosystems and their association with disease progression. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

9 Samples

Download data: MTX, TSV

(Submitter supplied) While advances in single cell genomics have helped to chart the cellular components of tumor ecosystems, it has been more challenging to characterize their specific spatial organization and functional interactions. Here, we combine single cell RNA-seq, spatial transcriptomics by Slide-seq, and in situ multiplex RNA analysis, to create a detailed spatial map of healthy and dysplastic colon cellular ecosystems and their association with disease progression. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

10 Samples

Download data: TAR, TXT

(Submitter supplied) Remyelination is reparative process by which axons that have lost their supportive insulation are re-encased in myelin. Multiple cell types are known to participate in this process, but their transcriptional dynamics from initial injury to full repair remain poorly characterized. Here, we combined high-throughput single-nucleus RNA-seq with Slide-seq, a high-resolution spatial transcriptomics technology, to densely reconstruct the cellular processes that coordinate remyelination after lysolecithin injection. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL24247

27 Samples

Download data: H5AD, H5SEURAT

(Submitter supplied) Animals adapt to environmental conditions by modifying the function of their internal organs, including the brain. To be adaptive, alterations in behavior must be coordinated with the functional state of organs throughout the body. Here we find that thyroid hormone--a regulator of metabolism in many peripheral organs--directly activates cell-type specific transcriptional programs in frontal cortex of adult male mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

49 Samples

Download data: MTX, TSV

(Submitter supplied) The zona incerta (ZI) plays an important role in diverse behavioral functions and is an emerging clinical target for deep brain stimulation to treat neurological conditions. Despite their importance, the cell type composition of the ZI and the anatomical circuit organization linking specific ZI cell types to brain-wide circuits remain unclear. In this study, we used single-nucleus RNA-sequencing, spatial RNA profiling, ex vivo electrophysiology, and anatomical circuit mapping to generate a multimodal cellular atlas of the ZI and to characterize the brain-wide monosynaptic inputs to specific ZI cell types. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

3 Samples

Download data: MTX, TSV

(Submitter supplied) Pediatric cancers are frequently driven by fusion or amplification events that result in aberrant transcription factor activity. As transcription factors themselves remain challenging to target, an emerging therapeutic approach for these cancers is to target epigenetic complexes that help maintain oncogenic transcriptional programs. It is therefore critical to identify the complete set of epigenetic modulators maintaining the oncogenic epigenetic landscape of pediatric cancers. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: BW

(Submitter supplied) Pediatric cancers are frequently driven by fusion or amplification events that result in aberrant transcription factor activity. As transcription factors themselves remain challenging to target, an emerging therapeutic approach for these cancers is to target epigenetic complexes that help maintain oncogenic transcriptional programs. It is therefore critical to identify the complete set of epigenetic modulators maintaining the oncogenic epigenetic landscape of pediatric cancers. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

35 Samples

Download data: BW

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21290 GPL24676

92 Samples

Download data

(Submitter supplied) Pediatric cancers are frequently driven by fusion or amplification events that result in aberrant transcription factor activity. As transcription factors themselves remain challenging to target, an emerging therapeutic approach for these cancers is to target epigenetic complexes that help maintain oncogenic transcriptional programs. It is therefore critical to identify the complete set of epigenetic modulators maintaining the oncogenic epigenetic landscape of pediatric cancers. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL21290

54 Samples

Download data: TXT

(Submitter supplied) The surge of antimicrobial resistance in recent decades threatens efficacy of current antibiotics, particularly against Pseudomonas aeruginosa, a highly resistant gram-negative pathogen. The asymmetric outer membrane of P. aeruginosa combined with its array of efflux pumps provide a barrier to xenobiotic intracellular accumulation, thus making the discovery of novel drugs with whole cell antibacterial activity very challenging. more...

Organism:

Pseudomonas aeruginosa UCBPP-PA14

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27892

30 Samples

Download data: CSV

(Submitter supplied) The surge of antimicrobial resistance in recent decades threatens efficacy of current antibiotics, particularly against Pseudomonas aeruginosa, a highly resistant gram-negative pathogen. The asymmetric outer membrane of P. aeruginosa combined with its array of efflux pumps provide a barrier to xenobiotic intracellular accumulation, thus making the discovery of novel drugs with whole cell antibacterial activity very challenging. more...

Organism:

Pseudomonas aeruginosa UCBPP-PA14

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27892

60 Samples

Download data: CSV

(Submitter supplied) MicroRNA (miRNA) maturation is critically dependent on structural features of primary transcripts (pri-miRNAs). However, the scarcity of determined pri-miRNA structures has limited our understanding of miRNA maturation. Here we employed SHAPE-MaP, a high-throughput RNA structure probing method, to unravel the secondary structures of 476 high-confidence human pri-miRNAs. Our SHAPE-based structures diverge substantially from those inferred solely from computation, particularly in the apical loop and basal segments, underlining the need for experimental data in RNA structure prediction. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL23227

12 Samples

Download data: CSV

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL21626 GPL24247

19 Samples

Download data: BW, TAB

(Submitter supplied) The loss of the tail is among the notable anatomical changes to have occurred along the evolutionary lineage leading to humans and to the “anthropomorphous apes”, with a hypothesized role in contributing to human bipedalism. Yet, the genetic mechanism that facilitated tail-loss evolution in hominoids remains unknown. Here, we present evidence that an individual insertion of an Alu element in the genome of the hominoid ancestor may have contributed to tail-loss evolution. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL21626

11 Samples

Download data: BW

(Submitter supplied) The loss of the tail is one of the main anatomical evolutionary changes to have occurred along the lineage leading to humans and to the “anthropomorphous apes”. This morphological evolution in the ancestral hominoids has long been considered to have accommodated a characteristic style of locomotion and contributed to the evolution of bipedalism in humans. Yet, the genetic mechanism that facilitated tail-loss evolution in hominoids remains unknown. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: TAB