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Comparison of gene expression profilling between iPS vs SSEA-1 positive or SSEA-1/3 negative sorted N417 cell line

ABSTRACT: To prove that hypoxia generates Cancer stem cells (CSCs) from non-CSCs, we needed to separate out already existing tumorigenic cells from the cell population. To identify CSCs, we used ES cell-specific cell surface antigens (SSEA-1, -3, -4, and Tra1-81) on the assumption that the immature cell fraction would be rich in CSCs. We analyzed the expression levels of such embryonic antigens and stemness genes in cells exposed to hypoxia.

ORGANISM(S): Homo sapiens

PROVIDER: GSE40842 | GEO | 2012/09/13

SECONDARY ACCESSION(S): PRJNA175065

REPOSITORIES: GEO

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Comparison of gene expression profilling between iPS vs SSEA-1 positive or SSEA-1/3 negative sorted N417 cell line

Project description:To prove that hypoxia generates Cancer stem cells (CSCs) from non-CSCs, we needed to separate out already existing tumorigenic cells from the cell population. To identify CSCs, we used ES cell-specific cell surface antigens (SSEA-1, -3, -4, and Tra1-81) on the assumption that the immature cell fraction would be rich in CSCs. We analyzed the expression levels of such embryonic antigens and stemness genes in cells exposed to hypoxia. iPS (253G1), SSEA-1 positive-N417 3 of SSEA-1/3 double negative-N417, each condition is represented by 3 biological replicates

2012-09-13 | E-GEOD-40842 | biostudies-arrayexpress

Expression data of MACS sorted cells (SSEA-1+ and SSEA-1-) from porcine fetal fibroblast cell line

Project description:A subset of cells in cellular populations may be preferentially reprogrammed into pluripotent stem cells due to their innate gene expression characteristics. SSEA-1+ sorted cells were shown to be more amenable to reprogramming than other cells in porcine fetal fibroblast cell lines. This microarray data reveals which genes are unique to the SSEA1+ sorted cells and helps to give them an identity. Porcine fetal fibroblasts were subjected to Magnetic Activated Cell Sorting using anti-SSEA-1. Five biological replicates were performed resulting in 5 SSEA-1 positive fractions and 5 SSEA-1 negative fractions which were analyzed.

2015-08-13 | E-GEOD-72025 | biostudies-arrayexpress

Transcription profile of SSEA-3-positive population of MSCs

Project description:Microarray analysis of the gene expression profile of SSEA-3-positive human adipose-derived MSCs were performed. Liposuction aspirates were obtained from the abdomen and thighs. Stromal vascular fraction (SVF) was isolated from the aspirated fat. Muse cells that express human SSEA-3 were collected from SVF using anti SSEA-3 antibody conjugated with PE and anti-PE microbeads. SSEA-3-negative fraction was considered M-bM-^@M-^XMuse-poor populationM-bM-^@M-^Y.

2015-01-07 | E-GEOD-55526 | biostudies-arrayexpress

Transcription profile of SSEA-3-positive population of MSCs

Project description:Microarray analysis of the gene expression profile of SSEA-3-positive human adipose-derived MSCs were performed.

2015-01-07 | GSE55526 | GEO

Expression data of MACS sorted cells (SSEA-1+ and SSEA-1-) from porcine fetal fibroblast cell line

2015-08-13 | GSE72025 | GEO

SSEA-4 labels a subset of poor prognosis-associated osteosarcoma-initiating cells that respond to differentiation induction

Project description:Osteosarcoma is thought of arising from the malignant transformation of osteogenic progenitors. The stage-specific embryonic antigen-4 (SSEA-4) labels a subset of TICs specially present in the high-risk subgroup. SSEA-4+ AND SSEA-4-

2014-06-05 | E-GEOD-58209 | biostudies-arrayexpress

SSEA-4 labels a subset of poor prognosis-associated osteosarcoma-initiating cells that respond to differentiation induction

2014-06-05 | GSE58209 | GEO

Human bone-derived 11Lin-CD45-CD271+SSEA-4+ mesenchymal stem/stromal cells from young and elderly patients

Project description:Global gene expressions of human bone-derived 11Lin-CD45-CD271+SSEA-4+ mesenchymal stem/stromal cells from young and elderly patients were analyzed. Results provide an insight into the molecular mechanisms of aging and cellular senescence.

2017-07-21 | GSE101694 | GEO

Time line RNAseq of iPSC-derived neurons from ASD and control subjects.

Project description:To comprehensively profile early neurodevelopmental alterations in individuals with ASD, we harnessed a time series approach to monitor patient-derived induced pluripotent stem cells (iPSCs) throughout the recapitulation of cortical development. This dataset consists of patient derived neurons that go through all consecutive developmental stages (NSC-derived neurons) as well as a comparative set of iPSC-iNs (neurons generated from the same patients that bypass early NSC-like stages using an Ngn2-transgene approach). For this, we first used fluorescence-activated cell sorting (FACS) to purify a homogeneous population of NSCs based on the expression of the cell-surface markers CD184+/CD271-/CD44-/CD24-/CD15+. To trace ASD and control neurons over time, we performed a series of retroviral lineage-tracing experiments to trace the progenies of dividing NSCs using a retroviral vector expressing a membrane-tagged enhanced green fluorescent protein (eGFP) (CAG::LckN-eGFP). As differentiating neurons express PSA-NCAM on the cell surface, we established a FACS-based protocol for purification of defined subpopulations of retrovirally labeled eGFP+/PSA-NCAM+ double-positive neurons after 2, 4, 7 and 14 days of differentiation. IPSCs were sorted based on the expression of SSEA-4 and TRA1-81 and maturing iPSC-iNs were collected at the indicated days after induction by sorting for eGFP (indicative for the Ngn2 transgene)- and PSA-NCAM-positive cells.

2019-01-07 | E-MTAB-6018 | biostudies-arrayexpress

GRIK2 is a target for bladder cancer stem-like cell-targeting immunotherapy

Project description:Recent studies revealed that treatment resistant cancer stem-like cells (CSCs)/cancer-initiating cells (CICs) can be targeted by cytotoxic T lymphocytes (CTLs). CTLs recognize antigenic peptide derived from tumor-associated antigens (TAAs), thus identification of tumor-associated antigens (TAAs) expressed in CSCs/CICs is essential. Human leucocyte antigen (HLA) ligandome analysis using mass spectrometry enables analysis of naturally expressed antigenic peptides; however, HLA ligandome analysis requires large scale of sample and it is challenging for CSCs/CICs. In this study, we established novel bladder CSC/CIC model from a bladder cancer cell line UM-UC-3 cells using ALDEFLUOR assay. CSCs/CICs were isolated as aldehyde dehydrogenase (ALDH) high cells and several ALDHhigh clone cells were established. ALDHhigh clone cells were enriched with CSCs/CICs by sphere formation and tumorigenicity in immune deficient mouse. HLA ligandome analysis and gene expression (CAGE) using ALDHhigh clone cells revealed distinctive antigenic peptide repertoire in bladder CSCs/CICs, and we identified GRIK2 derived antigenic peptide is specifically expressed in CSCs/CICs. GRIK2 peptide-specific CTL clone recognized GRIK2-overexpressed UM-UC-3 cells and ALDHhigh clone cells indicating that GRIK2 peptide can be a novel target for bladder CSCs/CICs-targeting immunotherapy.

2021-10-01 | GSE166947 | GEO

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