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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide expression profile on hiPSCs and hiPSC-derived CD33+ myeloid cells

ABSTRACT: To gain insights into which pathways might be dysregulated in JMML, we compared the transcriptome profiles among hiPSC and sorted CD33+ myeloid cells from control and patient samples. NS/JMML-derived CD33+ myeloid cells showed dysregulation in major biological processes. Moreover, a consistent expression pattern among sets of genes related to pluripotency and myeloid regulation was observed in the control, NS and NS/JMML CD33+ myeloid cells further supporting generally successful myelopoiesis. Total RNA obtained from hiPSC and sorted CD33+ myeloid cells (at day 14 of differentiation) from control and patient samples

ORGANISM(S): Homo sapiens

SUBMITTER: Angel Roman

PROVIDER: E-GEOD-54538 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide expression profile on hiPSCs and hiPSC-derived CD33+ myeloid cells

Project description:To gain insights into which pathways might be dysregulated in JMML, we compared the transcriptome profiles among hiPSC and sorted CD33+ myeloid cells from control and patient samples. NS/JMML-derived CD33+ myeloid cells showed dysregulation in major biological processes. Moreover, a consistent expression pattern among sets of genes related to pluripotency and myeloid regulation was observed in the control, NS and NS/JMML CD33+ myeloid cells further supporting generally successful myelopoiesis.

2014-01-31 | GSE54538 | GEO

Pretreatment with Gamma-Secretase Inhibitor Prevents Tumor-Like Overgrowth in Human iPSC-Derived Transplant for Spinal Cord Injury

Project description:Cell cycle- and more mature neuronal marker-related genes increased by > 2-fold change in both the GSI groups compared to the control group. To analyze gene expression profiles in hiPSC-NS/PCs treated with or without Gamma-secretase inhibitor.

2016-01-06 | E-GEOD-76556 | biostudies-arrayexpress

Inflammatory response in HSPC of PTPN11-mutated JMML

Project description:Activating mutations in PTPN11 gene are the most frequent in JMML patients. Here we explore the transcriptome of HSPC (hematopoietic stem and progenitor cells) sorted from sporadic JMML patients with PTPN11 mutation and from healthy age matched donnors. Bulk transcriptome of sorted HSPC reveals an inflammatory gene expression signature which may represent a future target for JMML therapy.

2021-09-06 | GSE183252 | GEO

Transcriptome and methylation analysis of JMML patients compare to healthy prenatal and postnatal samples.

Project description:JMML (Juvenile myelomonocytic leukaemia) is a leukaemia hat only develops in young children and is thought to have a prenatal initiation. To study the relationship between JMML and normal ontogeny we studied the transcriptome of HSPC (hematopoietic stem and progenitor cells) sorted from sporadic JMML patients, healthy prenatal samples and from healthy age matched donors. Bulk transcriptome of sorted HSPC reveals that some JMML samples cluster with prenatal samples whereas other from a distinct cluster apart from any healthy samples. Methylation profile on bulk mononucleated cell on theses JMML patients, 2 healthy postnatal and 2 healthy prenatal samples is also investigated. The results show a global hypermethylation in JMML samples compared to healthy samples and a specific JMML group with a hypermethylated profile compared to all JMML samples.

2022-12-31 | GSE198919 | GEO

Gene expression in human myeloid cells

Project description:Human myelopoiesis is an exciting biological model for cellular differentiation since it represents a plastic process where pluripotent stem cells gradually limit their differentiation potential, generating different precursor cells which finally evolve into distinct terminally differentiated cells. This study aimed at investigating the genomic expression during myeloid differentiation through a computational approach that integrates gene expression profiles with functional information and genome organization. The genomic distribution of myelopoiesis genes was investigated integrating transcriptional and functional characteristics of genes. The analysis of genomic expression during human myelopoiesis using an integrative computational approach allowed discovering important relationships between genomic position, biological function and expression patterns and highlighting chromatin domains, including genes with coordinated expression and lineage-specific functions. Keywords: cell differentiation Gene expression data from 20 experiments for 8 different cell types of the human myelopoietic lineage were used to generate an integrated myelopoiesis dataset.

2008-12-10 | E-GEOD-12803 | biostudies-arrayexpress

Single-cell RNA sequencing of human liver development and hiPSC models

Project description:scRNA-seq of primary human adult liver, primary human fetal liver (5 post conceptional weeks), EPCAM+ MACS sorted primary human intrahepatic duct cholangiocytes, sequential timepoints of hiPSC-derived hepatocyte-like cells (HLC), sequential timepoints of hiPSC-derived cholangiocyte-like cells (CLC), sequential timepoints of hiPSC-derived hepatic stellate-like cells (HSLC), sequential timepoints of hiPSC-derived endothelial-like cells (ELC), sequential timepoints of hiPSC-derived macrophage-like cells (MLC) and lentiviral transduced hiPSC-derived hepatocyte-like cells.

2022-05-04 | E-MTAB-8210 | biostudies-arrayexpress

Homo sapiens

Project description:Genome-wide expression profile on hiPSCs and hiPSC-derived CD33+ myeloid cells

| PRJNA237005 | ENA

Expression data from infant ALL with MLL-AF4 rearrangement

Project description:MLL-AF4+ blasts from infant B-ALL, CB-derived CD34+CD38-CD19-CD33- HSC, CB-derived CD34+CD19+CD33- B-cell HPCs and CB-derived CD34+CD33+CD19- myeloid HPCs. We used microarray to estudy gene expression profile comparing ALL vs HSC, HPC and myeloid HPSC. We used highly FACS-purified (purity>98%) MLL-AF4+ blasts from infant B-ALL, CB-derived CD34+CD38-CD19-CD33- HSC, CB-derived CD34+CD19+CD33- B-cell HPCs and CB-derived CD34+CD33+CD19- myeloid HPCs. For each independent sample technical duplicates were always performed. Total RNA was extracted using TRIol reagent, and quantified on a Nanodrop spectrophotometer and Bioanalyzer. High-quality RNA was reverse transcribed and the obtained cDNA was used as a template to synthesize biotinylanted cDNA, then was fragmented and hybridized as duplicates/triplicates to HG-U133 plus2.0 GeneChips (Affymetrix) according to manufacturer's guideline.

2016-03-22 | E-GEOD-79450 | biostudies-arrayexpress

HES2 embryonic stem cells (ESCs) grown in standard conditions and FACs sorted for GCTM-2 and CD9

Project description:HES2 ESCs were grown in standard ES culture conditions. After 1 week, these cells were FACs sorted for the presence of GCTM-2 and CD9. Keywords: Sorted cell comparison Three consecutive passages of HES2 cells were grown and subjected to FACs sorting. For each, 4 sorted populations of cells (p4, p5, p6, p7) were collected and these were subjected to microarray. A total of 12 samples: 3 replicates each of p4, p5, p6, and p7.

2010-04-08 | E-GEOD-13201 | biostudies-arrayexpress

Generation of Stem Cell-Derived Î² Cells from Type 1 Diabetic Patients

Project description:We recently reported the scalable in vitro production of functional stem cell-derived Î² cells. Here we extend this approach to generate SC-Î² cells from Type 1 diabetic patients (T1D), a cell type that is destroyed during disease progression and has not been possible to extensively study. These cells express Î² cell markers, respond to glucose both in vitro and in vivo, prevent alloxan-induced diabetes in mice, and respond to anti-diabetic drugs. Furthermore, we use an in vitro disease model to demonstrate the cells respond to different forms of Î² cell stress. Using these assays, we find no major differences in T1D SC-Î² cells compared to SC-Î² cells derived from non-diabetic patients (ND). These results show that T1D SC-Î² cells can be used for the treatment of diabetes, drug screening, and the study of Î² cell biology. Differentiated cells were sorted and processed for RNA isolation using the MARIS protocol published previously (PMID: 24516164.) Human induced pluripotent stem cell (hiPSC) line were differentiated into SC-beta cells or dysfunctional, polyhormonal cells (PH). Four biological replicates were assessed with differentiation to both SC-beta and PH cells. Those data were normalized together with and compared to existing, previously published data from Hrvatin et al. (PMID: 24516164) and Pagliuca et al. (PMID: 25303535) from human islet-derived insulin+ cells, undifferentiated HUES8 hES cells, SC-beta cells derived from HUES8 and PH cells derived from HUES8 according to previously published protocols.

2016-04-01 | E-GEOD-70901 | biostudies-arrayexpress

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