GEO DataSets

(Submitter supplied) Purpose: For patients with osteosarcoma, disease-related mortality most often results from lung metastasis—a phenomenon shared with many solid tumors. While established metastatic lesions behave aggressively, very few of the tumor cells that reach the lung will survive. By identifying mechanisms that facilitate survival of disseminated tumor cells, we can develop therapeutic strategies that prevent and treat metastasis. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25526 GPL25431

5 Samples

Download data: TAR

(Submitter supplied) Recently, cell therapy has emerged as a promising treatment option for various disorders. Given the intricate mechanisms of action (MOA) and heterogenous distribution in target tissues inherent to cell therapy, it is necessary to develop more sophisticated, unbiased approaches to evaluate the distribution of administered cells and the molecular changes at a microscopic level. This study introduces a label-free approach for assessing the tissue distribution of administered human mesenchymal stem cells (hMSCs) and their MOA, leveraging spatially resolved transcriptomics (ST) analysis. more...

Organism:

Mus musculus; Homo sapiens

Type:

Other

Platforms:

GPL21103 GPL25431

5 Samples

Download data: TAR

(Submitter supplied) Six-week old Fah−/−/Rag2−/−/Il2rg −/− (FRG) –NOD breeding mice were intravenously injected with 1.5 x 10^9 plaque forming units (pfu) of an adenoviral vector encoding the secreted form of the human urokinase-like plasminogen activator (Ad-uPA). Forty-eight hours later, 10^6 PHH were injected intrasplenically. Successfully transplanted mice were fed with CDA-HFD for 16 weeks and then treated with humanized CLDN1 specific mAb 500 µg or vehicle for additional 8 weeks. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25431

10 Samples

Download data: TSV

(Submitter supplied) To investigate the functional role of EGFR in the formation of large vessels, we established a mesenchymal glioma stem cell line (GSC83) with intact EGFR and knocked down EGFR by Crispr-Cas9. We then performed single cells gene expression profiling analysis using data obtained from RNA-seq of 2 different tumours, derived by injection of GSC83 WT or GSC83 KO in NSG mice. In addition, GSC83 WT or GSC83 KO tumours in NSG mice were subjected to spatial gene expression profiling in situ using GeoMX platform. more...

Organism:

Homo sapiens; Mus musculus; synthetic construct

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24247 GPL26526 GPL25431

45 Samples

Download data: DCC, PKC, RDS, TAR, XLSX

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

12 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) We used single-cell RNA-sequencing to investigate the role of brain-resident microglia versus infiltrating cells in a mouse model of breast cancer brain metastasis (BCBM). We generated brain metastases with a cardiac-injection of the human triple-negative breast cancer cell line MDA-MB-231BR2 (231BR) into Foxn1 nu/nu mice and allowed tumors to grow in the brain for four weeks. We then compared astrocytes (ASCA2+CD45-) and myeloid cells (CD11b+CD45+) from these mice verses control Foxn1 nu/nu brains to find transcriptional changes associated with BCBM.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21103 GPL25431

6 Samples

Download data: MTX, TSV, TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL25431 GPL30173

101 Samples

Download data: MTX, SF, TSV

(Submitter supplied) Breast cancer is the most commonly diagnosed cancer among women. PDXs (patient-derived xenografts) are similar to cancer cell lines but differ in that they are maintained in a physiological setting as soon as they are isolated from the patient and for subsequent passages. These models are valuable for preclinical trials because PDX models have been shown to closely match their patient counterparts, both in genomic profile and response to treatment. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25431

76 Samples

Download data: SF

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

Organism:

Mus musculus; Homo sapiens

Type:

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

Platforms:

GPL25431 GPL20301

40 Samples

Download data: BED

(Submitter supplied) Renal medullary carcinoma (RMC) is an aggressive tumour driven by bi-allelic loss of SMARCB1 and tightly associated with sickle cell trait. However, the cell-of-origin and oncogenic mechanism remain poorly understood. Using single-cell sequencing of human RMC, we defined transformation of thick ascending limb (TAL) cells into an epithelial-mesenchymal gradient of RMC cells associated with loss of renal epithelial transcription factors TFCP2L1, HOXB9 and MITF and gain of MYC and NFE2L2-associated oncogenic and ferroptosis resistance programs. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL25431

4 Samples

Download data: TSV

(Submitter supplied) We report the differential RNA expression and splicing variants in xenografted AITL cells and the associated mouse stromal cells in the lymph node of 3 CXCR5-antagonist-treated mice and 3 vehicle-treated mice

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25431

6 Samples

Download data: BED, CSV, TXT

(Submitter supplied) We present a new approach, Light-Seq, for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding in fixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially-targeted, rapid photocrosslinking of DNA barcodes onto cDNAs in situ with a novel one-step DNA stitching reaction to create pooled, spatially-indexed sequencing libraries. This light-directed barcoding enables in situ selection of multiple cell populations in intact fixed tissue samples for full transcriptome sequencing based on location, morphology, or protein stains, without cellular dissociation. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25431 GPL16417 GPL24247

14 Samples

Download data: CSV

(Submitter supplied) The MYC oncogene encodes for the MYC protein and is frequently dysregulated across multiple cancer cell types, making it an attractive target for cancer therapy. MYC overexpression leads to MYC binding at active enhancers, resulting in a global transcriptional amplification of active genes. Since superenhancers are frequently dysregulated in cancer, we hypothesized that MYC preferentially invades into superenhancers and alters the cancer genome organization. more...

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL16791 GPL15520 GPL25431

28 Samples

Download data: HIC, NARROWPEAK, TSV, TXT

(Submitter supplied) Our aim was to investigate the contribution of TWIST1 on Neuroblastoma (NB) tumor formation and dissemination using TWIST1 knock-out (KO) in the SK-N-Be2C cell line.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25431 GPL20301

19 Samples

Download data: CSV

(Submitter supplied) RNA-sequencing data of the prostate cancer xenograft PC346C-DCC-K model. Tumor bearing mice were treated daily with Enzalutamide (N=10, 60mg/kg) or placebo (N=5, vehicle) for a period of 7 days. Tumor were subsequently isolated and snap-frozen. Tumor tissue was lysed and homogenized in QIAzol (ref #79306, Qiagen, Hilden, Germany) using an Ultra-Turrax T25 (Janke & Kunkel, Staufen, Germany). Total RNA was isolated using the miRNA-easy mini kit (ref # 217004, Qiagen), and RNA quality was measured using the Bioanalyzer RNA 6000 Nano assay (ref #5067, Agilent, Santa Clara, California, USA). more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25431

15 Samples

Download data: TXT

(Submitter supplied) Luciferase and GFP labeled Du145 prostate cancer cells were injected into the left cardiac ventricle of CB17 SCID mice and allowed to grow until tumors were detectable in bones. FACS was used to isolate prostate cancer cells as described (Cackowski et al, J Cellular Biochemistry 2017) from bones with detectable tumor or the remaining pelvis, lumbar vertebrae, femorae, tibiae and humorae which had tumor cells present but below the limit of detection by imaging. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25431

4 Samples

Download data: TXT

(Submitter supplied) Single nuclei sequencing of grafts developed 14 weeks post transplantation of human embryonic stem cell derived pancreatic progenitors alone (PP) or with rat adipose derived microvessels (PPMV) into the subcutaneous pocket of diabetic (STZ-induced) Scid-beige mice.

Organism:

Homo sapiens; Rattus norvegicus; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25431 GPL30035

2 Samples

Download data: CSV

(Submitter supplied) Astrocytes were purified from mouse cortices and human cortex tissue by immunopanning with HepaCAM. All treatments were proceeded on 3DIV in serum-free medium. Astrocytes were treated by TNFα for 48hr, by Poly I:C for 72hr, or by hypoxia for 72hr. Acutely purified atrocytes RNA was harvest immediately after HepaCAM immunopanning. Serum selected astrocytes RNA was collected after 4-6 days culturing in serum medium. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

77 Samples

Download data: XLSX

(Submitter supplied) Two mice in which luciferase-positive LOUCY ETP-ALL cells were xenografted were treated with either vehicle or ABT-199 (50 mg/kg) for 11 days. Afterwards, single cells suspensions were made from bone marrow and spleen of both mice for 10x Genomics scRNA-seq. Following quality control, a total of 13,681 spleen cells and 11,442 bone marrow cells of the control mouse and 15,955 spleen cells and 9,443 bone marrow cells of the ABT 199 treated mouse were processed for further analysis. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25431

4 Samples

Download data: H5

(Submitter supplied) Pluripotent cells of the mammalian embryo undergo extensive chromatin rewiring to prepare for lineage commitment after implantation. Repressive H3K27me3, deposited by Polycomb Repressive Complex 2 (PRC2), is reallocated from large blankets in pre-implantation embryos to mark promoters of developmental genes. The regulation of the global redistribution of H3K27me3 is poorly understood. Here we report a post-translational mechanism that destabilizes PRC2 to constrict H3K27me3 during lineage commitment. more...

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL21103 GPL25431 GPL19057

37 Samples

Download data: BW, TXT