Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nextflow Pipeline for Visium and H&E Data from Patient-Derived Xenograft Samples

ABSTRACT: Nextflow Pipeline for Visium and H&E Data from Patient-Derived Xenograft Samples

PROVIDER: PRJNA997362 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR25387786_1.fastq.gz	Fastqsanger.gz
	SRR25387786_2.fastq.gz	Fastqsanger.gz
	SRR25387787_1.fastq.gz	Fastqsanger.gz
	SRR25387787_2.fastq.gz	Fastqsanger.gz
	SRR25387788_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Nextflow Pipeline for Visium and H&E Data from Patient-Derived Xenograft Samples

Project description:We designed a Nextflow DSL2-based pipeline, Spatial Transcriptomics Quantification (STQ), for simultaneous processing of 10x Genomics Visium spatial transcriptomics data and a matched hematoxylin and eosin (H&E)-stained whole slide image (WSI), optimized for Patient-Derived Xenograft (PDX) cancer specimens. Our pipeline enables the classification of sequenced transcripts for deconvolving the mouse and human species and mapping the transcripts to reference transcriptomes. We align the H&E WSI with the spatial layout of the Visium slide and generate imaging and quantitative morphology features for each Visium spot. The pipeline design enables multiple analysis workflows, including single or dual reference genomes input and stand-alone image analysis. We show the utility of our pipeline on a dataset from Visium profiling of four melanoma PDX samples. The clustering of Visium spots and clustering of H&E imaging features reveal similar patterns arising from the two data modalities.

2024-05-21 | GSE238004 | GEO

Texas Pediatric Patient Derived Xenograft

Project description:Texas Pediatric Patient Derived Xenograft

| PRJNA939343 | ENA

RNA-Seq of patient derived osteosarcoma xenograft samples

Project description:RNA-Seq of patient derived osteosarcoma xenograft samples

| PRJNA513353 | ENA

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

RNA-Seq of patient derived osteosarcoma xenograft samples

Project description:Observing the gene expression of ATRX, DAXX, H3F3A, SMARCAL1, SLX4IP and TERT in 7 patient derived osteosarcoma xenograft samples (Houghton et al., 2007) which are using the Alternative Lengthening of Telomere (ALT) pathway.

2019-09-01 | GSE124768 | GEO

Proteomic Profiling of Breast Cancer Patient-Derived Xenograft

Project description:Mass spectrometry profiling of orthotopically transplanted breast cancer patient-derived xenograft (PDX) tumors prior to chemotherapy treatment.

2022-12-06 | PXD035857 | Pride

Patient-derived xenograft platform for metastatic melanoma

Project description:Patient-derived xenograft platform for metastatic melanoma

| PRJNA297786 | ENA

Mayo GBM Patient Derived Xenograft National Resource

Project description:Mayo GBM Patient Derived Xenograft National Resource

| PRJNA548580 | ENA

Construction of GBM patient-derived xenograft mouse models

Project description:Our adult GBM patient-derived xenograft mouse models keep the genomics characteristics of GBM patient tumors.

2023-07-12 | GSE207886 | GEO

Construction of GBM patient-derived xenograft mouse models

Project description:Construction of GBM patient-derived xenograft mouse models