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Ena-DATASET-dkfz_b062-04-08-2017-13:47:34:208-1428 - samples

ABSTRACT: Whole exome sequencing data to 30 PDOX models (28 early passages, 3 late passages (1 overlap)), 3 cell lines, and 20 matching human tumors

PROVIDER: EGAD00001003544 | EGA |

REPOSITORIES: EGA

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ena-DATASET-dkfz_b062-04-08-2017-14:15:21:871-1439 - samples

Project description:Low-coverage whole genome sequencing data for 30 PDOX models (28 early passages, 4 late passages (2 overlaps)), 3 cell lines, and 21 matching human tumors

| EGAD00001003545 | EGA

Single Cell Sequencing Reveals Gene Expression Signatures Associated with Bone Marrow Stromal Cell Subpopulations and Time in Culture [microarray]

Project description:Background Bone marrow stromal cells (BMSCs) are a heterogeneous population that participates in wound healing, immune modulation and tissue regeneration. Next generation sequencing was used to analyze transcripts from single BMSCs in order to better characterize BMSC subpopulations. Methods Cryopreserved passage 2 BMSCs from one healthy subject were cultured through passage 10. The transcriptomes of bulk BMSCs from designated passages were analyzed with microarrays and RNA sequencing (RNA-Seq). For some passages, single BMSCs were separated using microfluidics and their transcriptomes were analyzed by RNA-Seq. Results Transcriptome analysis microarray and RNA-Seq of unseparated BMSCs from passages 2, 4, 6, 8, 9 and 10 yielded similar results; both data sets grouped passages 4 and 6 and passages 9 and 10 together and genes differentially expressed among these early and late passage BMSCs were similar. 3D Diffusion map visualization of single BMSCs from passages 3, 4, 6, 8 and 9 clustered passage 3 and 9 into two distinct groups, but there was considerable overlap for passage 4, 6 and 8 cells. Markers for early passage, FGFR2, and late passage BMSCs, PLAT, were able to identify three subpopulations within passage 3 BMSCs; one that expressed high levels of FGFR2 and low levels of PLAT; one that expressed low levels of FGFR2 and high levels of PLAT and one that expressed intermediate levels of FGFR2 and low levels of PLAT. Conclusions Single BMSCs can be separated by microfluidics and their transcriptome analyzed by next generation sequencing. Single cell analysis of early passage BMSCs identified a subpopulation of cells expressing high levels of FGFR2 that might include skeletal stem cells.

2019-01-10 | GSE124860 | GEO

Single Cell Sequencing Reveals Gene Expression Signatures Associated with Bone Marrow Stromal Cell Subpopulations and Time in Culture [NGS_bulk cell RNA-seq]

2019-01-10 | GSE124859 | GEO

Single Cell Sequencing Reveals Gene Expression Signatures Associated with Bone Marrow Stromal Cell Subpopulations and Time in Culture [scRNA-seq]

2019-01-10 | GSE124858 | GEO

CGH analysis of an extramedullary muletiple myeloma PDX

Project description:A patient derived orthotopic xenograft (PDOX) was generated from a patient with an aggressive EMM to study in-depth genetic and epigenetic events and drug responses related to extramedullary disease. One of these studies was the evaluation of genetic imbalances by Affymetrix Cytoscan 750K array. The PDOX was derived from a fresh punch of an extramedullary cutaneous lesion that was orthotopically implanted in a NSG mouse. The PDOX mimicked histologic and phenotypic features of patient’s tumor. Cytogenetic studies revealed a hyperploid genome with multiple genetic poor-prognosis alterations. Copy number alterations were detected in all chromosomes.

2021-06-18 | E-MTAB-10630 | biostudies-arrayexpress

scRNA-seq profiling of tumor microenvironment in glioblastoma patient-derived orthotopic xenogratfs (PDOXs)

Project description:Single-cell RNA-sequencing was performed on the tumor microenvironment of the glioblastomas isolated from PDOX models (Golebiewska et al., Acta Neuropathologica, 2020; Oudin et al., STAR Protocols 2021). Sample names correspond to PDOX models. Normal mouse brain was used as a contol. One PDOX model was treated with temolozomide (P3TMZ).

2023-03-07 | GSE226468 | GEO

ena-DATASET-dkfz_b062-18-08-2017-15:54:03:183-161 - samples

Project description:RNA sequencing data for the PDOX model EPD-613FH

| EGAD00001003573 | EGA

Data expression of young and senescent human mesenchymal stem cells (hMSC).

Project description:The transcriptome of hMSC in late passages was compared to hMSC in early passages. Both hMSC were obtained from the umbilical vein of three donors, two of hMSC have a normal karyotype (MSC/n) and another has a constitutional paracentric chromosomal inversion (hMSC/inv).

2014-12-30 | GSE56530 | GEO

ena-DATASET-MPIMG-07-11-2016-14:00:41:902-798 - samples

Project description:RNAseq on Illumina HiSeq2000/2500 of PDO culture derived from colorectal cancer metastasis sample at early/late passages

| EGAD00001002884 | EGA

Transcriptional profiling of mouse ovarian surface epithelial cells during in vitro spontaneous transformation

Project description:Mouse ovarian surface epithelial (MOSE) cells were isolated from adult C57BL6 female mice and cultured during 28 passages in a standard medium. Total RNA was analyzed with NIA-15K microarrays.

2016-11-16 | GSE81729 | GEO

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