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Transcription profiling of human freshly isolated adipose-derived adult stem cells (ADASCs) vs cultured cells

ABSTRACT: In order to assess whether culturing adipose-derived adult stem cells (ADASCs) affect their gene expression (see Sample Growth Condition Protocol), we wanted to identify possible genes that were differentially expressed between cultured polyclonal CD31- ADASCs and freshly isolated (uncultured) polyclonal CD31- ADASCs. To that end, RNA was isolated from cultured and uncultured ADASCs from three different donors and analyzed using the Affymetrix Microarray HG-U133A. Then, using the Affymetrix program MAS 5.0 we performed three comparisons and could identify differentially expressed transcripts common between the three donors, using the Affymetrix program DMT 3.0.

ORGANISM(S): Homo sapiens

SUBMITTER: Katrine Fronsdal

PROVIDER: E-MEXP-168 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Isolation and transcription profiling of purified uncultured human stromal stem cells: alteration of gene expression after in vitro cell culture.

Boquest Andrew C AC Shahdadfar Aboulghassem A Frønsdal Katrine K Sigurjonsson Olafur O Tunheim Siv H SH Collas Philippe P Brinchmann Jan E JE

Molecular biology of the cell 20050105 3

Stromal stem cells proliferate in vitro and may be differentiated along several lineages. Freshly isolated, these cells have been too few or insufficiently pure to be thoroughly characterized. Here, we have isolated two populations of CD45-CD34+CD105+ cells from human adipose tissue which could be separated based on expression of CD31. Compared with CD31+ cells, CD31- cells overexpressed transcripts associated with cell cycle quiescence and stemness, and transcripts involved in the biology of ca ...[more]

PMID: 15635089

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Transcription profiling of freshly isolated CD31+ vs freshly isolated CD31- adipose-derived adult stem cells (ADASCs)

Project description:In order to assess whether there were differences in gene expression between the polyclonal CD31+ and the polyclonal CD31- cell populations of adipose-derived adult stem cells (ADASCs), we wanted to identify possible genes that were differentially expressed between these two cell populations. To that end, RNA was isolated from polyclonal CD31+ and the polyclonal CD31- ADASCs from three different donors and analyzed using the Affymetrix Microarray HG-U133A. Then, using the Affymetrix program MAS 5.0 we performed three comparisons and could identify differentially expressed transcripts common between the three donors, using the Affymetrix program DMT 3.0.

2004-09-27 | E-MEXP-167 | biostudies-arrayexpress

Expression data from tumor-associated endothelial cells of hepatocellular carcinoma

2013-10-19 | GSE51401 | GEO

Expression data from tumor-associated endothelial cells of hepatocellular carcinoma

Project description:Primary uncultured CD31+ and CD105+ tumor endothelial cells (TEC), non-tumor endothelial cells (NEC) ,remnant cells from tumor (TC) and non-tumor liver tissue (NTC)of HCC tissues from patientswere isolated by magnetic-activated cell sorting. Affymetrix Human Gene ST Arrays were used to determine gene expression profiles of HCC cells and matched TEC and NEC cells. We use the gene expression profiling of the Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA) to identify distinct genes of TEC and NEC. Patient specimens were collected immediately after removal from patients with pathologically proven HCC and positive alpha-fetoprotein (AFP), then washed 3 times by phosphate buffer solution (PBS). Single cell suspension was obtained from separated tumor and non-tumor liver tissues of surgical specimens following the protocol (http://www.miltenyibiotec.com), then CD31+ cells or CD105+ cells were isolated using CD31 antibody or CD105 antibody conjugated magnetic beads in autoMACSpro (Meltenyi biotec).After the sample preparation, the gene expression profiling was performed using the Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA) according to manufacturerM-bM-^@M-^Ys protocols at ShanghaiBio Corporation (Shanghai, China).

2013-10-19 | E-GEOD-51401 | biostudies-arrayexpress

Transcriptome analysis of HUVEC

Project description:Human umbilical vein endothelial cells (HUVEC) were isolated from umbilical cords from four different donors, as previously described (Cooke et al., 1993). Cells were maintained in Medium 199 (M199, Invitrogen) containing 20% fetal calf serum, 28g/ml gentamycin, 2.5g/ml amphotericin B, 1ng/ml epidermal growth factor and 1g/ml hydrocortisone (all from Sigma) for 48 hours prior to processing. HUVEC cultures isolated using this method were 96-98% pure, determined by positive staining by flow cytometry of CD105, CD31 and vWF and the expression of elevated levels of intracellular adhesion molecule (ICAM-1) and E-selectin following stimulation with the inflammatory cytokine interleukin-1. Total HUVEC RNA was isolated using the RNeasy mini kit with QIAshredder (Qiagen) according to the manufacturers instructions. RNA integrity number was >8.0 for all samples.

2016-09-30 | E-MTAB-4897 | biostudies-arrayexpress

Knockout of CNOT1 and CNOT10 in primary CD4+ T-cells causes a type-1 interferon response

Project description:We report a type 1 interferon response accompanying polyclonal knockout of CNOT1 or CNOT10 in primary human CD4+ T-cells harvested from healthy donors

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Comparison of periosteal, adipose, and dermal CD146+ human pericytes

Project description:Human pericytes demonstrate multilineage differentiation potential, and their descendants participate in tissue homeostasis and repair. Increasing evidence from developmental biology and tissue engineering suggest that regional specification by tissue of origin exists among human pericytes. Here, we sought to define the differentiation of CD146+ human pericytes from skeletal and soft tissue sources. Uncultured CD146+CD31-CD45- pericytes were derived by fluorescent activated cell sorting from human periosteum, adipose, or dermal tissue. Periosteal CD146+CD31-CD45- cells retained canonical features of pericytes, including cell surface marker expression, multilineage differentiation potential, and paracrine induced tubulogenesis. Periosteal pericytes demonstrated a striking tendency to undergo osteoblastogenesis, while soft tissue pericytes did not in vitro or in vivo. Microarray analysis demonstrated substantive differences between periosteal pericytes in comparison to their soft tissue pericyte counterparts. In sum, skeletal and soft tissue pericytes differ in their relative lineage differentiation potential and ability to form bone. Human tissues were microdissected, digested, and FACS sorted to derived a CD146+CD31-CD45- pericyte population, and cells were expanded in standard growth medium (DMEM, 10% FBS, 1% pen/strep) and nucleic acid isolated at subconfluency

2021-08-01 | GSE118962 | GEO

Genome-wide analysis of DNA methylation and gene expression patterns in purified, uncultured human liver cells and activated hepatic stellate cells

Project description:The human liver contains multiple cell types whose epigenetic patterns are undetermined. We examined the promoter methylome of purified and uncultured hepatic stellate cells (HSCs), hepatocytes (HEPs) and liver sinusoidal endothelial cells (LSECs), by methylated DNA immunoprecipitation (MeDIP) and array hybridization. Uncultured HSCs, LSECs and Heps show ~7000-8000 methylated promoters, with 60-70% similarity between all cell types. GO analysis for commonly methylated genes reveals involvement in germ cell development, segregating germ-line from somatic lineage methylation. HSCs, LSECs and HEPs also contain ~500-1000 uniquely methylated promoters; these are implicated in signaling and biosynthetic processes (HSCs), lipid transport and metabolism (LSECs), and chromatin assembly (HEPs). The promoter methylome of culture-activated HSCs deviates from that of their uncultured (quiescent) counterparts. HSC culture-induced activation also enhances methylation differences between individual donors; however this does not necessarily relate to changes in gene expression. HSc activation results in a net gain of promoter DNA methylation, despite the demethylation and de novo methylation of thousands of promoters. Our data provide to our knowledge the first genome-wide maps of promoter DNA methylation in human purified and uncultured liver cell types. Although methylation profiles are largely similar between HSCs, LSECs and hepatocytes, the detection of cell type-specific methylation patterns suggests a differential epigenetic programming of these cell types in the liver.

2015-12-21 | GSE66796 | GEO

FACS sorting of human adipose tissue stromal vascular fraction

Project description:Adipose tissue from 6 non-obese patients was collagenase treated and adipocytes separated from the stromal vascular fraction(SVF). SVF was then FACS sorted for the following fractions CD45-/CD34+/CD31+ (endothelial), CD45-/CD34+/CD31- (progenitor), CD45+/CD14+ (monocyte/macrophage), CD45+/CD14-(Leukocyte). RNA was isolated from adipocyte, SVF, progenitor, macrophage/monocyte and leukocyte fractions and analyzed on the Affymetrix Human Transcriptome 2.0 array. We also sorted SVF from an additional 13 (10 non-obese, 9 obese) patients and sent progenitor RNA for Affymetrix Human Transcriptome 2.0 array analysis.

2017-09-19 | GSE80654 | GEO

Whole-transcriptome analysis of endothelial-to-hematopoietic stem cell transition

Project description:Hematopoietic stem cells (HSCs) are generated via a natural transdifferentiation process known as endothelial-to-hematopoietic cell transition (EHT). Due to small numbers of embryonal arterial cells undergoing EHT and the paucity of markers to enrich for hemogenic endothelial cells, the genetic program driving HSC emergence is largely unknown. Here, we use a highly sensitive RNAseq method to examine the whole transcriptome of small numbers of enriched aortic HSCs (CD31+cKit+Ly6aGFP+), hemogenic endothelial cells (CD31+cKit-Ly6aGFP+) and endothelial cells (CD31+cKit-Ly6aGFP-).

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Genome-wide analysis of DNA methylation and gene expression patterns in purified, uncultured human liver cells and activated hepatic stellate cells

2015-12-21 | E-GEOD-66796 | biostudies-arrayexpress