Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole transcriptome profiling of 79 patient derived xenograft (PDX) models

ABSTRACT: RNA-Seq and a species-specific mapping strategy were used to profile the human and mouse transcriptomes of tumour samples taken from 79 PDX models representing multiple cancer types (19 x breast, 37 x lung, 8 x colorectal, 7 x ovarian, 3 x endometrial, 2 x pancreatic, 2 x ampullary, 1 x leukaemia).

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER: James Bradford

PROVIDER: E-MTAB-3980 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Affymetrix GeneChip Human Genome U133 Plus 2.0 array expression analysis of patient-derived xenografts in NSG mice

Project description:To provide a snapshot of gene expression for the cancer models distributed by The Jackson Laboratory as assayed using the Affymetrix HU133 platform.

2021-12-17 | E-MTAB-9063 | biostudies-arrayexpress

RNA-seq expression analysis of patient-derived xenografts in NSG mice

Project description:To provide a snapshot of gene expression for the cancer models distributed by The Jackson Laboratory.

2021-12-17 | E-MTAB-9153 | biostudies-arrayexpress

Stranded RNA-seq expression analysis of patient-derived xenografts in NSG mice

Project description:To provide a snapshot of gene expression for the cancer models distributed by The Jackson Laboratory.

2021-12-17 | E-MTAB-9204 | biostudies-arrayexpress

Integrative analysis of non-small cell lung cancer patient-derived xenografts identifies unique proteotypes associated with patient outcomes

Project description:We generated PDX models of aggressive NSCLC, which represent the DNA methylation features modelling of primary NSCLC

2021-11-24 | E-MTAB-10156 | biostudies-arrayexpress

Secretome identification of immune cell factors mediating metastatic cell homing

Project description:Metastatic cell homing is a complex process mediated in part by diffusible factors secreted from immune cells found at a pre-metastatic niche. We report on connecting together secretomics and a TRanscriptional Activity CEll aRray (TRACER) to identify functional paracrine interactions between immune cells and metastatic cells as novel mediators of metastatic cell homing. Splenocytes from orthotopic mouse models of breast cancer were isolated to generate a diseased splenocyte conditioned media (D-SCM) containing immune cell secreted factors. MDA-MB-231 metastatic cell activity including cell invasion, migration, transendothelial migration, and proliferation were increased when cultured with D-SCM compared to healthy SCM (H-SCM) and unconditioned media controls. Our secretome analysis of D-SCM yielded secreted factor candidates that contribute to increased metastatic cell activity. In parallel, we identified active TFs within metastatic cells in response to the secreted factors using TRACER. We connected both data sets using MetaCore software to determine interactions between immune cell secreted factors and active metastatic cell TFs to narrow down functional secreted factor candidates that mediate metastatic cell homing. Haptoglobin was among the list of secreted factors and was validated in vitro as a key mediator of metastatic cell recruitment. Furthermore, we designed an implantable poly(lactide-co-glycolide) biomaterial scaffold as a mimic of the pre-metastatic niche to slowly release haptoglobin and demonstrate increased homing of metastatic cells to the scaffold in vivo. Taken together, our studies demonstrate a novel systems biology technique to identify functional paracrine signaling factors, which were validated to reveal mediators of metastatic cell homing.

2015-12-17 | PXD002051 | Pride

Label-free proteomics quantification of pancreatic ductal adenocarcinoma patient-derived xenografts with treatment combining Gemcitabine and nab-Paclitaxel

Project description:Tumor-stroma interactions are critical in pancreatic ductal adenocarcinoma (PDAC) progression and therapeutics. Patient-derived xenograft (PDX) models faithfully recapitulate tumor-stroma interactions in PDAC, but conventional antibody-based immunoassay is largely inadequate to resolve or quantify tumor and stromal proteins. A species-deconvolved proteomics approach embedded in the ultra-high-resolution (UHR)-IonStar workflow can unambiguously quantify the proteins from tumor (human-derived) and stroma (mouse-derived) in PDX samples, enabling unbiased investigation of their proteomes with excellent quantitative reproducibility. With this strategy, 3 PDAC PDXs were analyzed. They were showed differential responses to treatment with Gemcitabine combined with nab-Paclitaxel (GEM+PTX), which is a first-line treatment regimen for PDAC. For each PDAC PDX, samples were collected after 24 hour and 192 hour with/without treatment, and each condition contained four biological replicates.

2023-07-05 | PXD042267 | Pride

Pharmacological inhibition of TREM1 attenuates patient derived xenograft models

Project description:To characterize the transcriptional changes in PDX tumors during TREM1 inhibition by microarray

2023-09-27 | E-MTAB-13257 | biostudies-arrayexpress

Affimetrix Gene 1.0 ST array expression analysis of patient-derived xenografts in NSG mice

Project description:To provide a snapshot of gene expression for the cancer models distributed by The Jackson Laboratory.

2021-12-17 | E-MTAB-8859 | biostudies-arrayexpress

Medulloblastoma Patient-Derived Xenograft Proteomics

Project description:Proteomic and phosphoproteomic characterization of 20 orthotopic patient-derived xenograft models of medulloblastoma

2022-09-01 | PXD035070 | Pride

Characterizing the Chemoresistant Ovarian Cancer Population using the Heterogeneous PDX

Project description:The patient-derived xenograft (PDX) model retains the heterogeneity of patient tumors, allowing a means to not only examine efficacy of a therapy across a population, but also study crucial aspects of cancer biology in response to treatment. Herein we describe the development and characterization of an ovarian-PDX model in order to study the development of chemoresistance. We demonstrate that PDX tumors are not simply composed of tumor-initiating cells, but recapitulate the original tumor’s heterogeneity, oncogene expression profiles, and clinical response to chemotherapy. Combined carboplatin/paclitaxel treatment of PDX tumors enriches the cancer stem cell populations, but persistent tumors are not entirely composed of these populations. RNA-Seq analysis of treated PDX tumors compared to untreated tumors demonstrates a consistently contrasting genetic profile after therapy, suggesting similar, but few, pathways are mediating chemoresistance. The pathways most significantly altered included Protein Kinase A signaling, GNRH signaling, and sphingosine-1-phosphate signaling. Pathways and genes identified by this methodology represent novel approaches to targeting the chemoresistant population in ovarian cancer 6 pairs of Patient-Derived Xenografts (PDX) were ananlyzed using RNA-seq for a total of 12 samples. Each pair consists of a treated and untreated PDX of ovarian cancer. Treated Ovarian cancer PDXs were treated with 4 weeks of a combination of carboplatin and taxol. RNA was isolated and converted to cDNA. RNA-seq was conductred on the Illumina HiSeq 2000 with 50 bp paired end sequencing

2015-06-17 | E-GEOD-58586 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data