Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene Expression Profiles of tumor sorted fractions demarcating genetic instability using DNA-RNA content based cell cycle analysis in ovarian cancer xenograft tumor

ABSTRACT: Our earlier report states role of genetic instability and aneuploid cells in drug resistance and tumor recurrence. Hence segregating tumor based on DNA content is a good model to study genetic in stability. We have earlier reported isolation of cell line (A4T) from a patient with Grade IV serous adenocarcinoma (Bapat et al. Cancer Research. 2005). Xenograft generated by injecting A4T cells in NOD/SCID mice exhibited genetic instability (Kusumbe and Bapat Cancer Research. 2009; Naik et.al Oncogene 2015). We generated xenograft by injecting 2.5x106 A4T P65 s.c in NOD/SCID mice. Mice were observed for tumor formation and tumors were harvested at day 28 (4 weeks) and processed for collagenase digestion for preparation of single cell suspension. Further cells were subjected to staining with Hoechst (33342) for 45min at 37˚C followed by pyronin Y for 45min at 37˚C and processed for FACS sorting. Staining profile was acquired on BD FACS Aria II across UV laser for Hoechst and PE channel for PyroninY with linear scale. Details of the Hoechst pyronin Y based ploidy and cell cycle analysis are published in our earlier reports (Kusumbe and Bapat Cancer Research. 2009; Naik et.al Oncogene 2015). DNA content of cell line injected is considered as euploid while the higher genetic content is called as aneuploid.

ORGANISM(S): Homo sapiens

PROVIDER: GSE74852 | GEO | 2016/01/01

SECONDARY ACCESSION(S): PRJNA301679

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Gene Expression Profiles of tumor sorted fractions demarcating genetic instability using DNA-RNA content based cell cycle analysis in ovarian cancer xenograft tumor

Project description:Our earlier report states role of genetic instability and aneuploid cells in drug resistance and tumor recurrence. Hence segregating tumor based on DNA content is a good model to study genetic in stability. We have earlier reported isolation of cell line (A4T) from a patient with Grade IV serous adenocarcinoma (Bapat et al. Cancer Research. 2005). Xenograft generated by injecting A4T cells in NOD/SCID mice exhibited genetic instability (Kusumbe and Bapat Cancer Research. 2009; Naik et.al Oncogene 2015). We generated xenograft by injecting 2.5x106 A4T P65 s.c in NOD/SCID mice. Mice were observed for tumor formation and tumors were harvested at day 28 (4 weeks) and processed for collagenase digestion for preparation of single cell suspension. Further cells were subjected to staining with Hoechst (33342) for 45min at 37ËC followed by pyronin Y for 45min at 37ËC and processed for FACS sorting. Staining profile was acquired on BD FACS Aria II across UV laser for Hoechst and PE channel for PyroninY with linear scale. Details of the Hoechst pyronin Y based ploidy and cell cycle analysis are published in our earlier reports (Kusumbe and Bapat Cancer Research. 2009; Naik et.al Oncogene 2015). DNA content of cell line injected is considered as euploid while the higher genetic content is called as aneuploid. Euploid and aneuploid were sorted with 99% purity and 1x105 cells from each fraction was subjected to RNA isolation, labeling and microarray analysis. RNA of each fraction was labeled with Cy3 and designated as A4Euploid and A4Aneuploid. Three samples of each were chosen for hybridization.

2016-07-03 | E-GEOD-74852 | biostudies-arrayexpress

RNA-Seq of human intracranially implanted U87MG-GFP cells as a function of distance from blood vessels

Project description:We devised a novel methodology for sorting stroma-free tumor cells according to their relative distance from BVs by injecting a vascular perfusion marker (Hoechst 33342). Briefly, post 3 weeks of intracranial implantation of U87MG-GFP cell line into striatum of NOD-SCID mice, the mice were injected i.v. with Hoechst dye. Mice sacrificed, tumors retrieved, single cell dissociated and FACS sorted to isolate cells that are either Hoechst Positive (Hh) or Hoechst Negative (Hl). RNA was extracted from the sorted cells and RNA-Sequencing performed.

2019-04-30 | E-MTAB-6881 | biostudies-arrayexpress

RNA-Seq of human U87MG-GFP cells from sub-cutan xenografts as a function of distance from blood vessels

Project description:We devised a novel methodology for sorting stroma-free tumor cells according to their relative distance from BVs by injecting a vascular perfusion marker (Hoechst 33342). Briefly, post 4 weeks of sub cutaneous implantation of U87MG-GFP cell line into dorsal flank of NOD-SCID mice, the mice were injected i.v. with Hoechst dye. Mice sacrificed, tumors retrieved, single cell dissociated and FACS sorted to isolate cells located at progressive distance from blood vessels based on perfusion dye intake. Three fractions namely - Hh (close to BVs), Hm (intermediate) and Hl (farther from BVs) were FACS sorted. RNA was extracted from the sorted cells and RNA-Sequencing performed.

2019-04-29 | E-MTAB-6882 | biostudies-arrayexpress

RNA-seq of human U87MG-GFP perivascular glioma stem cells

Project description:Glioblastoma stem cells (GSCs) have been reported to be found near the blood vessels. We wanted to identify the perivascular GSCs by combining the label retention approach with vascular perfusion. GSCs, like most of the stem cells, are in a quiescent state. Label retention approach involves staining the cells with a uniform membrane labeling dye (PKH26) and allowing them to grow in vivo in NOD SCID mice. Slow-dividing stem cells will retain the dye to a greater extent and perivascular cells are identified by injecting the mice with vascular perfusion dye (Hoechst 33342) 5 min prior to sacrifice. Perivascular GSCs (positive for Hoechst 33342 and pKH26 dye - dubbed as H+P+) were compared with the rest of the perivascular glioma cells (H+P-).

2022-01-01 | E-MTAB-9607 | biostudies-arrayexpress

Cross-Linking/mass spectrometry (CLMS) analysis of RNA polymerase II

Project description:The mass spectrometry data of a previous publication (Chen et.al. 2009 doi:10.1038/emboj.2009.401) were reprocesed and is used for method developing, teaching and training purpose.

2018-07-20 | PXD010481 | Pride

Cross-Linked/Mass-spectrometry analysis of RNA-Polimerase II

Project description:The data of a previous publication (Chen et.al. 2009 doi:10.1038/emboj.2009.401) where reprocesed and then used to validate false discovery rate calculations for unique residue pairs.

2017-03-09 | PXD004749 | Pride

Gene Expression Profiles of tumor sorted fractions demarcating cancer stem cell heirarchy using PKH dye in ovarian cancer xenograft tumor

Project description:Our earlier report states isolation of ovarian cancer stem cell heirarchy using membrane labeling PKH26/67 dyes (Kusumbe and Bapat Cancer Research. 2009) in a xenograft model. We earlier reported that ovarian cancer is a stem cell disease with isolation of cell line (A4T) from a patient with Grade IV serous adenocarcinoma (Bapat et al. Cancer Research. 2005). A4T cells were labelled with PKH26 membrane labeling dye, flourescence intensity was quantified and set as 100% dye retaining cells (PKHhi) with flow cytometery. 2.5x10^6 P65 A4PKH26 labeled cells were injected s.c in NOD/SCID mice, while unlabeled cells were also injected for generation of control tumors . Mice were observed for tumor formation and tumors were harvested at day 28 (4 weeks) and processed for collagenase digestion for preparation of single cell suspension. Tumor cells were acquired on BD FACS Aria II across PE channel of blue laser. Cells retaining dye intensity as that of preinjected cells were gated as PKHhi while cells exhibiting complete dye depletion were gated as PKHneg using unlabeled tumor cells as control; while cells showing intermediate label intensity were gated as PKHlo. Details of the flow cytometry analysis and sorting are published in our earlier reports (Kusumbe and Bapat Cancer Research. 2009).

2016-01-01 | GSE74851 | GEO

Gene Expression Profiles of tumor sorted fractions demarcating cancer stem cell heirarchy using PKH dye in ovarian cancer xenograft tumor

2016-07-03 | E-GEOD-74851 | biostudies-arrayexpress

Chromosome copy number changes in Mps1DK-driven p53 null T-ALL samples

Project description:Mps1DK and p53 loss were combined in T-cells specificely leading to early onset and highly aggressive aneuploid T-ALL. Tumors were characterized for (recurrrent) copy number changes with a focus on whole chromosome abnormalities. DNA content was compared to the DNA content of sex-matched uninfiltrated control liver samples from litter mates

2014-07-01 | GSE57331 | GEO

Chromosome copy number changes in Mps1DK-driven p53 null T-ALL samples

2014-07-01 | E-GEOD-57331 | 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