GEO DataSets

(Submitter supplied) The human gut includes plasma cells (PCs) expressing immunoglobulin A1 (IgA1) or IgA2, two structurally distinct IgA subclasses with elusive regulation, function and reactivity. We show here that intestinal IgA1+ and IgA2+ PCs co-emerged early in life, comparably accumulated somatic mutations, and were enriched within short-lived CD19+ and long-lived CD19− PC subsets, respectively. IgA2+ PCs were often clonally related to IgA1+ PCs and a subset of them presumably emerged from IgA1+ precursors. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

1 Sample

Download data: CSV, MTX, TSV

(Submitter supplied) The goal of this study was to compare the gene expression program of liver iNKT1 cells from Control mice to those with a postselection deletion of the transcription factor Ets1 and heterozybous deletion of Tbx21. Ets1-floxed and Tbx21-floxed alleles were deleted in iNKT1 cells using Tbx21Cre bacterial artifical chromosome transgenic mice that also carry a Rosa26-floxed-stop-YFP reporter. Control iNKT1 cells were Tbx21Cre+ Rosa26-floxed-stop-YFP reporter+ and cKOHet iNKT cells were Tbx21Cre+ Ets1F/F Tbx21F/+ Rosa26-floxed-stop-YFP reporter+. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: TXT

(Submitter supplied) Tumor-educated platelets (TEPs) are a potential method of liquid biopsy for the diagnosis and monitoring of cancer. However, the mechanism underlying tumor education of platelets is not known, and transcripts associated with TEPs are often not tumor-associated transcripts. We demonstrate that direct tumor transfer of transcripts to circulating platelets is an unlikely source of the TEP signal. We use CDSeq, a latent Dirichlet allocation algorithm, to deconvolute the TEP signal in blood samples from patients with glioblastoma. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24247

4 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Tumor-educated platelets (TEPs) are a potential method of liquid biopsy for the diagnosis and monitoring of cancer. However, the mechanism underlying tumor education of platelets is not known, and transcripts associated with TEPs are often not tumor-associated transcripts. We demonstrate that direct tumor transfer of transcripts to circulating platelets is an unlikely source of the TEP signal. We use CDSeq, a latent Dirichlet allocation algorithm, to deconvolute the TEP signal in blood samples from patients with glioblastoma. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

9 Samples

Download data: TXT

(Submitter supplied) We previously found that an adeno-associated virus (AAV) vector containing S. aureus Cas9 and a multi-target guide (g)RNA could integrate into the genome and prematurely terminate transcription of Ube3a-ATS, a long non-coding RNA. Here, we assessed the performance of three additional AAV vectors containing S. aureus Cas9 and twenty-five vectors containing N. meningococcus Cas9, all targeting single sites within Ube3a-ATS. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL23969

60 Samples

Download data: XLSX

(Submitter supplied) Despite lingering genotoxicity concerns, CRISPR-based genome editing has progressively entered the gene therapy field. Here we report that interactions between nucleotide sequences that are localized on the same chromosome and exhibit a high degree of homology contribute substantially to post-editing chromosomal rearrangements. We successfully employed corrective editing strategies at the NCF1 gene, as well as at the colocalized pseudogenes, NCF1B and NCF1C, in a human cell line model of p47phox-deficient chronic granulomatous disease and in patient-derived human hematopoietic stem cells. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

7 Samples

Download data: XLSX

(Submitter supplied) Plant nitrate, phosphate, and sucrose responses create a complex molecular network fine-tuned for growth and survival. This triangular interplay, crucial for the adaptability of terrestrial plants, allows the availability of one nutrient to influence plant responses to others. However, the origins and functional repurposing of this complex network for plant terrestrialization remain scarcely understood. more...

Organism:

Marchantia polymorpha; Klebsormidium nitens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28764 GPL30306

125 Samples

Download data: CSV

(Submitter supplied) Rab35 knockdown results in a loss of apical bulkheads from hepatocytes, which causes isotropic growth of the bile canaliculus (BC) and ultimately results in the formation of hepatocyte cysts. In these cysts, hepatocytes have common apico-basal polarity, such as observed for simple epithelia like cholangiocytes. To investigate whether this change in polarization is associated with alterations in gene expression we compared hepatocytes with and without Rab35 knockdown in a previous RNA-sequencing experiment and found changes in gene expression after 5 days of culture. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

45 Samples

Download data: TAB

(Submitter supplied) The ability of individual cells to maintain a distinct identity and respond to transient environmental signals requires tightly controlled regulation of gene networks. However, how discrete sets of gene regulators coordinate circuits that respond to extracellular cues remains poorly defined. The need for context-dependent regulation is prominent in human CD4+ T cells, where distinct cell lineages must respond to diverse signals to orchestrate effective adaptive immune responses and maintain homeostasis. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL34281

24 Samples

Download data: CSV, MTX, TSV

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL14951 GPL13534

160 Samples

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(Submitter supplied) Prognosis for cardiogenic shock patients under ECMO was our study goal. Success defined as survived more than 7 days after ECMO installation and failure died or had multiple organ failure in 7 days. Total 34 cases were enrolled, 17 success and 17 failure. Peripheral blood mononuclear cells collected at ECMO installation 0, 2 hours and removal were analyzed.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

82 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

5 related Platforms

443 Samples

Download data: BED, BEDGRAPH, BIGWIG, NARROWPEAK

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

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL24247

21 Samples

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(Submitter supplied) Self-renewal programs in leukemia stem cells (LSCs) predict poor prognosis in acute myeloid leukemia (AML) patients. We identified CD4+ T cell-derived interleukin (IL) 21 as an important negative regulator of self-renewal of murine and human LSCs, but not hematopoietic stem cells. IL21/IL21R signaling favored asymmetric cell division and differentiation in LSCs through accumulation of reactive oxygen species (ROS) and activation of p38-MAPK signaling, resulting in reduced LSCs number and significantly prolonged survival in murine AML models. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

7 Samples

Download data: XLSX

(Submitter supplied) Self-renewal programs in leukemia stem cells (LSCs) predict poor prognosis in acute myeloid leukemia (AML) patients. We identified CD4+ T cell-derived interleukin (IL) 21 as an important negative regulator of self-renewal of murine and human LSCs, but not hematopoietic stem cells. IL21/IL21R signaling favored asymmetric cell division and differentiation in LSCs through accumulation of reactive oxygen species (ROS) and activation of p38-MAPK signaling, resulting in reduced LSCs number and significantly prolonged survival in murine AML models. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: XLSX

(Submitter supplied) The SKOV3 cells were treated with carboplatin or a combination of carboplatin and COM33 for 48h. The cells were lysed by TRIzol and total RNA was used for library construction. After cluster generation, the library preparations were sequenced on an Illumina HiSeq 4000 platform by Shanghai Life Genes Biotech Co. Ltd (Shanghai, China), and 150 bp paired-end reads were generated. After processing, filtering and checking quality, differentially expressed genes (DEGs) were screened using the following criteria: P < 0.05 and absolute log2 (fold change) > 1.0.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

9 Samples

Download data: TXT

(Submitter supplied) We developed an unbiased strategy for MOA prediction, called Perturbation-Specific Transcriptional Mapping (PerSpecTM), in which large-throughput expression profiling of wildtype or hypomorphic mutants, depleted for essential targets, enables a computational strategy to address this challenge. We applied PerSpecTM to perform reference-based MOA prediction based on the principle that similar perturbations, whether small molecule or genetic, will elicit similar transcriptional responses. more...

Organism:

Pseudomonas aeruginosa UCBPP-PA14

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27892

1059 Samples

Download data: CSV

(Submitter supplied) Clonotype selection of T cell receptors (TCRs) have been the core component of TCR therapy development. However, the conventional and widely used major histocompatibility complex (MHC) multimer staining technologies focus on high-affinity interactions between TCR and MHC-antigen complex, which may fail to identify TCRs with high efficacy for activating T cells. Here, we developed the Aptamer-based T Lymphocyte Activity Screening and sequencing (ATLAS-seq) method on a microfluidic platform. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

19 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) The goal of this study was to compare the gene expression program of thymic and liver iNKT1 cells from Control mice to those with a postselection deletion of the transcription factor Ets1. Ets1-floxed alleles were deleted in iNKT1 cells using Tbx21Cre bacterial artifical chromosome transgenic mice that also carry a Rosa26-floxed-stop-YFP reporter. Control iNKT1 cells were Tbx21Cre+ Rosa26-floxed-stop-YFP reporter+. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL34290 GPL24676 GPL24247

234 Samples

Download data: TXT