GEO DataSets

(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

(Submitter supplied) Children with relapsed or refractory T-cell acute lymphoblastic leukemia (T-ALL) have a poor prognosis with few therapeutic options. Multiple lines of evidence point towards the enzyme dihydroorotate dehydrogenase (DHODH) as a metabolic vulnerability in dysregulated and malignant T‑cells. DHODH catalyzes the fourth step of de novo pyrimidine nucleotide synthesis (e.g., uridine, cytidine). Therefore, inhibiting DHODH via small molecule inhibitors (DHODHi) rapidly leads to the depletion of intracellular pyrimidine pools and forces cells to rely on extracellular salvage. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: TXT

(Submitter supplied) Genome-wide association studies (GWAS) have discovered thousands of risk loci for common, complex diseases, each of which could point to genes and gene programs that influence disease. For some diseases, it has been observed that GWAS signals converge on a smaller number of biological programs, and that this convergence can help to identify causal genes. However, identifying such convergence remains challenging: each GWAS locus can have 2-20 candidate genes, the cellular programs a gene participates in are difficult to define in an unbiased fashion, and it remains unclear which genes and programs would be likely to influence disease risk. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

24 Samples

Download data: TXT

(Submitter supplied) We previous identified enhancers that regulate MYC expression in K562 cells (Fulco et al. Science 2016). Here, we perturbed MYC enhancers with individual CRISPRi gRNAs and performed ChIP-seq to study the effects on chromatin state.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

54 Samples

Download data: TDF

(Submitter supplied) We report the results of bulk RNA-seq from human Hürthle cell carcinoma (HCC) samples and matched normal thyroids. The bulk RNA-seq data reveals the molecular programs that are activated in HCC. These activated programs include mTOR and Myc signaling, the mitochondrial unfolded protein response, lipid peroxide scavenging, and amino acid biosynthesis.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

42 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

Platform:

GPL24247

591 Samples

Download data: MTX, RESULTS, TSV

(Submitter supplied) To identify which brain cell types are contributing to the bulk transcriptomic changes in Grin2a mutant mice, we performed single-nucleus RNAseq (snRNAseq) in Grin2a heterozygous and homozygous mutants and their wild-type littermates at 4 and 12 weeks of age.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

83 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) To investigate the effect of Grin2a (a schizophrenia risk gene) and Grin2b (an autism spectrum disorder risk gene) loss of function on brain transcriptome. We performed unbiased transcriptomic profiling (bulk RNAseq analysis) in 5 brain regions and at four postnatal ages in Grin2a and Grin2b mutant mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

508 Samples

Download data: RESULTS

(Submitter supplied) Using thisapproach, wequeriedthe pan-cancer vulnerability landscape upon activating 10key pathway nodes, revealing selectiveactivation dependenciesof MAPK and PI3K pathwaysassociatedwith specific biomarkers

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

66 Samples

Download data: CSV

(Submitter supplied) To investigate effect of WNT hyperactivation by CTNNB1 overexpression or APC knockdown on gene expression and probe possible mechanism of cell viability effect, we overexpressed GFP/CTNNB1, or induce knockdown of APC by shNT1 (non-targeting) and shAPC

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: CSV

(Submitter supplied) Cytokines mediate cell-cell communication in the immune system and represent important therapeutic targets. While there have been in-depth studies of individual cytokines, we lack a global view of the responses of each major immune cell type to each cytokine. To address this gap we created the Immune Dictionary — a compendium of single-cell transcriptomic profiles of over 17 immune cell types in response to each of 86 cytokines in murine lymph nodes in vivo. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

88 Samples

Download data: MTX, TSV, XLSX

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL19057 GPL24247

120 Samples

Download data: H5

(Submitter supplied) Immune checkpoint blockade is effective for some cancer patients, but most are refractory to current immunotherapies and new approaches are needed to overcome resistance. The protein tyrosine phosphatases PTPN2 and PTPN1 are central regulators of inflammation, and their genetic deletion in either tumour or immune cells promotes anti-tumour immunity. However, phosphatases are challenging drug targets and in particular, the active site has been considered undruggable. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: CSV

(Submitter supplied) Immune checkpoint blockade is effective for some cancer patients, but most are refractory to current immunotherapies and new approaches are needed to overcome resistance. The protein tyrosine phosphatases PTPN2 and PTPN1 are central regulators of inflammation, and their genetic deletion in either tumour or immune cells promotes anti-tumour immunity. However, phosphatases are challenging drug targets and in particular, the active site has been considered undruggable. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: TXT

(Submitter supplied) To examine the effect of AC484 inhibition on the tumor immune microenvironment, we performed scRNA-seq on CD45+ cells from B16 and KPC tumors from mice treated with vehicle, anti-PD-1, or AC484.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

28 Samples

Download data: H5