GEO DataSets

(Submitter supplied) Fibrosis is regulated by interactions between immune and mesenchymal cells. However, the capacity of cell types to modulate human fibrosis pathology is poorly understood due to lack of a fully humanized model system. MISTRG6 mice were engineered by homologous mouse/human gene replacement to develop an immune system like humans when engrafted with human hematopoietic stem cells (HSC) (1, 2). We utilized MISTRG6 mice to model scleroderma by transplantation of healthy or scleroderma skin from a patient with pansclerotic morphea to humanized mice engrafted with unmatched allogeneic HSC. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22245

6 Samples

Download data: H5

(Submitter supplied) To determine how exposure to CHOP, Selinexor or their combination affects gene expression in DLBCL, we first established a patient-derived xenograft model of DLBCL. Next, mice were randomized to receive either vehicle, CHOP, Selinexor or their combination. Tumors were harvested at the end of treatment and gene expression profile analyzed by RNA-sequencing.

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22245

12 Samples

Download data: ZIP

(Submitter supplied) Changes in the three-dimensional (3D) structure of the genome are an emerging hallmark of cancer. However, little is known about the rewiring of the 3D chromatin landscape during cancer progression to a chemotherapy-resistant state. We utilized a patient-derived xenograft (PDX) mouse model of triple-negative breast cancer (UCD52) to characterize changes in the 3D structure between the primary tumor and carboplatin-resistant state. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22245

6 Samples

Download data: TXT

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

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL22245 GPL26363

8 Samples

Download data: HIC, TXT

(Submitter supplied) This study is a repository for all RNAseq data obtained from High Throuput Seqeuncing of Patient Derived Xenograft models of Breast Cancer studied at the Baylor College of Medicine Breast Center.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

153 Samples

Download data: RESULTS, TXT

(Submitter supplied) Chromatin profiling at locus resolution uncovers gene regulatory features that define cell types and developmental trajectories, but it remains challenging to map and compare distinct chromatin-associated proteins within the same sample. Here we describe a scalable antibody barcoding approach for profiling multiple chromatin features simultaneously in the same individual cells, Multiple Target Identification by Tagmentation (MulTI-Tag). more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL18573 GPL16791 GPL22245

171 Samples

Download data: BEDGRAPH, BW, PDF

(Submitter supplied) The brain is a major sanctuary site for metastatic lung cancer cells that evade systemic therapies. We performed pharmacological, biological, and molecular studies to identify the functional link between drug resistance and central nervous system (CNS) relapse in late-stage EGFR mutant non-small cell lung cancer, which frequently progresses in the brain even when treated with the brain penetrant EGFR inhibitor osimertinib. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22245 GPL16791

35 Samples

Download data: TXT

(Submitter supplied) We found that ERY974 shows only moderate antitumor efficacy in NCI-H446 non-inflamed tumor in huNOG mice. We also observed that ERY974 + cisplatin increases antitumour efficacy in non-inflamed NCI-H446 tumours. To identify a mechanism of combination effect, we compared RNA expression of NCI-H446 tumors treated with ERY974, cisplatin, or combination.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22245

36 Samples

Download data: XLSX

(Submitter supplied) GPC3 expression is one of the important predictive marker of ERY974. However, we found that efficacy of ERY974 is sometimes different in tumors with the similar GPC3 expression. To identify a predictive biomrker of ERY974, we compared baseline RNA expression of tumors in which ERY974 shows moderate efficacy, and/or achives the regression with similar GPC3 expression.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22245

24 Samples

Download data: XLSX

(Submitter supplied) We found that ERY974 shows only moderate antitumor efficacy in NCI-H446 non-inflamed tumor in huNOG mice. We also observed that ERY974 + paclitaxel increases antitumour efficacy in non-inflamed NCI-H446 tumours. To identify a mechanism of combination effect, we compared RNA expression of NCI-H446 tumors treated with ERY974, cisplatin, or combination.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22245

38 Samples

Download data: XLSX

(Submitter supplied) We found that ERY974 shows only moderate antitumor efficacy in MKN45 non-inflamed tumor in huNOG mice. We also observed that ERY974 + capecitabine increases antitumour efficacy in non-inflamed MKN45 tumours. To identify a mechanism of combination effect, we compared RNA expression of MKN45 tumors treated with ERY974, capecitabine, or combination.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22245 GPL25526

24 Samples

Download data: XLSX

(Submitter supplied) Fate decisions in the embryo are controlled by a plethora of microenvironmental interactions in a three-dimensional niche. To investigate whether aspects of this microenvironmental complexity can be engineered to direct myogenic human induced pluripotent stem cell (hiPSC) differentiation, we screened cell types present in the developmental or adult stem cell niche in heterotypic suspension embryoids. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL17021 GPL22245

24 Samples

Download data: CSV

(Submitter supplied) Lymphoma cells interact with specific microenvironment cell subsets, such as stromal cells, from which they receive survival and proliferation stimuli. These interactions negatively influence therapeutic response and increase the risk for drug resistance and relapse. It is still not clear why clinically similar tumors in different patients respond differently to established treatment regimens. Objective: The main aim of this study was to identify and compare key signaling pathways related to stromal cell adhesion in different mantle cell lymphoma (MCL) cell lines.Methods: Human MCL cells (JeKo1 and REC1) were cultured alone or in co-culture with mouse MS-5 stromal cells. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL22245 GPL16791

16 Samples

Download data: CSV

(Submitter supplied) Circulating nucleic acids, encapsulated within exosomes, can provide a remote cellular snapshot of biomarkers associated with disease, however selective exosome isolation is critical. Current laboratory-based purification techniques rely on the physical properties of exosomes for selection, rather than their inherited cellular characteristics. Therefore, we established a highly selective purification assay, termed exosome Capture by AnTibody of CHoice and Enzymatic Release (exo-CATCHER), designed for high-throughput analysis of low-abundance small-RNA cargos by next-generation sequencing. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL17021 GPL22245

74 Samples

Download data: XLSX

(Submitter supplied) Hypermethylation of helicase-like transcription factor (HLTF) in colorectal cancer (CRC) cells occurs more frequently in men than women. Progressive epigenetic silencing of HLTF in tumor cells is accompanied by negligible expression in the tumor microenvironment (TME). Cell line-derived xenografts were established in control (Hltf+/+) and Hltf-deleted male Rag2-/-IL2rg-/- mice by direct orthotopic microinjection of HLTF+/+HCT116 cells into the submucosa of the cecum. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22245

6 Samples

Download data: XLSX

(Submitter supplied) We performed RNA sequencing experiments on chimeric samples of mixed human and mouse pluripotent stem cells over time courses of neural differentiation.

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL17021 GPL22245

1067 Samples

Download data: TAB

(Submitter supplied) Single-cell RNA sequencing in principle offers unique opportunities to improve the efficacy of contemporary T-cell based immunotherapy against cancer. The use of high-quality single-cell data will aid our incomplete understanding of molecular programs determining the differentiation and functional heterogeneity of cytotoxic T lymphocytes (CTLs) allowing for optimal therapeutic design. So far a major obstacle to high depth single-cell analysis of CTLs is the minute amount of RNA available leading to low capturing efficacy. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL22245

27 Samples

Download data: CSV, FA, MTX, TSV, TXT

(Submitter supplied) In situ assays of transcription factor (TF) binding are confounded by cellular heterogeneity and represent averaged profiles in complex tissues. Single cell RNA-seq (scRNA-seq) is capable of resolving different cell types based on gene expression profiles, but no technology exists to directly link specific cell types to the binding pattern of TFs in those cell types. Here, we present self-reporting transposons (SRTs) and their use in single cell calling cards (scCC), a novel assay for simultaneously capturing gene expression profiles and mapping TF binding sites in single cells. more...

Organism:

Mus musculus; Homo sapiens

Type:

Other

8 related Platforms

27 Samples

Download data: BAM, CSV, LOOM, TSV, TXT

(Submitter supplied) In many solid tumors, tissue of mesenchymal subtype is frequently associated with epithelial-mesenchymal transition (EMT) state, strong stromal infiltration, and poor prognosis. Emerging evidence from tumor ecosystem studies indicate that the stromal components, including cancer associated fibroblast (CAFs), actively participate in cancer growth and progression. Transcriptomic analysis of xenograft tissues provides a unique advantage in dissecting hallmark genes of tumor (human) or stromal (murine) origins.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22245 GPL19415

11 Samples

Download data: TXT

(Submitter supplied) It has been reported that mesenchymal stem cells (MSC) derived from adult tissues are effective in promoting wound healing. However, the cell quality varies and cell number is limited as both depend on donations. Moreover, dissociated MSC delivered to an inflammatory lesion are subject to challenges to their survival and functions. Here we demonstrate that dropping of spheres of MSC derived from human embryonic stem cells (EMSC) onto murine dermal wound had much higher survival and efficacy than topical application of dissociated EMSC. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22245 GPL17021 GPL16791

15 Samples

Download data: XLSX