Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from quiescent cells and cycling cells isolated from Multicellular aggregates of lymphoma cells (MALC)

ABSTRACT: Follicular Lymphomas are blood tumors growing as spheres in patients. Before this study, there was no experimental model mimicking the 3D organization of these in vivo tumors. We develop such a model, called MALC, and observed a progressive enrichment in quiescent cells in these with time of culture; these cells were sorted, as their cycling counterparts, and their transcriptomes were compared. We used microarrays to detail the differential global gene expression profile between quiescent and cycling cells isolated from MALC.

ORGANISM(S): Homo sapiens

PROVIDER: GSE41855 | GEO | 2012/10/27

SECONDARY ACCESSION(S): PRJNA178329

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Expression data from quiescent cells and cycling cells isolated from Multicellular aggregates of lymphoma cells (MALC)

Project description:Follicular Lymphomas are blood tumors growing as spheres in patients. Before this study, there was no experimental model mimicking the 3D organization of these in vivo tumors. We develop such a model, called MALC, and observed a progressive enrichment in quiescent cells in these with time of culture; these cells were sorted, as their cycling counterparts, and their transcriptomes were compared. We used microarrays to detail the differential global gene expression profile between quiescent and cycling cells isolated from MALC. 14 days-old MALC were stained with pyronin Y and quiescent and cycling subpopulations sorted were selected for RNA extraction and hybridization on Affymetrix U133+ 2.0 microarrays.

2012-10-27 | E-GEOD-41855 | biostudies-arrayexpress

Expression data from follicular lymphoma cells cultured either in suspension either as Multicellular aggregates of lymphoma cells (MALC)

Project description:Follicular Lymphomas are blood tumors growing as spheres in patients. Before this study, there was no experimental model mimicking the 3D organization of these in vivo tumors. We develop such a model, called MALC, and performed a pan-genomic comparative analysis between MALC and classical suspension cultures. We used microarrays to detail the global gene expression profile induced by aggregated growth of lymphoma cells. 10 days-old MALC and suspension RL cells were selected for RNA extraction and hybridization on Affymetrix U133+ 2.0 microarrays.

2012-10-27 | E-GEOD-41851 | biostudies-arrayexpress

Expression data from follicular lymphoma cells cultured either in suspension either as Multicellular aggregates of lymphoma cells (MALC)

2012-10-27 | GSE41851 | GEO

Transcription profiling of human BRAFE600-induced senescent, senescence bypassing, and quiescent fibroblast cells, compared to cycling cells

Project description:Analysis of BRAFE600-induced senescent, senescence bypassing, and quiescent cells, all compared to cycling cells.

2008-06-13 | E-NCMF-12 | biostudies-arrayexpress

RNA-sequencing of cycling PKH26-Negative cells and PKH26-Positive label retaining quiescent cancer stem cells from colon cancer patient-derived organoids

Project description:Recent data suggests that colon tumors contain a subpopulation of therapy resistant quiescent cancer stem cells (qCSCs) are the source of relapse following treatment. The isolation and molecular characterisation of qCSCs may therefore lead to the identification of novel therapeutic targets for their elimination. Label retention of the lipophilic fluorescent dye PKH26, wherein dividing cells lose the label and quiescent or slow cycling cells retain the label for an extended period of time, was used to isolate qCSCs from a panel of colon cancer patient-derived organoids (PDOs). PDOs were dissociated to single cells, labelled with PKH26 and plated in Matrigel culture. After 12 days, PDOs were processed to single cells, labelled with DAPI (to exclude dead cells) and isolated by fluorescence assisted cell sorting (FACS) into two fractions of PKH26-Negative and PKH26-Positive (label retaining) cells. Functional analyses of these cellular subpopulations demonstrated that PKH26-Positive cells are self-renewing qCSCs. RNA was collected from FAC sorted PKH26-Negative and PKH26-Positive cells and analysed by RNA-sequencing. Cells were lysed in RLTplus buffer and RNA was extracted using Qiagen RNeasy Mini Kit. RNA quality was assessed prior to sequencing. Samples were processed using NuGEN’s Ovation RNA-Seq System V2 and Ultralow V2 Library System and sequenced on an Illumina HiSeq 2500 machine as 2x125nt paired-end reads. Reads were mapped to the human reference genome (assembly hg19) using the STAR aligner (version 2.4.2a). Total read counts per gene were computed using the program “featureCounts” (version 1.4.6-p2) in the “subread” package, with the gene annotation taken from Gencode (version 19).

2021-02-08 | E-MTAB-8924 | biostudies-arrayexpress

HMEC Quiescent single cells

Project description:Gene expression after mammosphere culture, quiescent single cells

| EGAD00010001964 | EGA

Molecular characterization of quiescent melanoma cells

Project description:Cancer dormancy is closely associated with cellular quiescence, a state whereby cells exit the cell cycle and are reversibly arrested in G0 phase. Curative cancer treatment thus requires therapies that either sustain the dormant state of quiescent cancer cells, or preferentially, eliminate them. However, the mechanisms responsible for the quiescent survival of these cells remain obscure. We took advantage that quiescent cells characteristically negative for the proliferation marker Ki67 and express high levels of the cyclin-dependent kinase (CDK) inhibitor p27 to develop a CRISPR/Cas9-based system to fuse a green fluorescent protein (EGFP) gene with endogenous CDKN1B, the gene encoding p27, and a red fluorescent protein (mCherry) gene with endogenous MKI67, the gene encoding Ki67 in the genome of human melanoma cells. Flow cytometry were used to isolate the viable quiescent (p27high/Ki67low) cells. The isolated quiescent and cycling cancer cells were subjected to RNA-seq

2021-05-18 | GSE174520 | GEO

Slow Cycling and Durable Flt3+ Progenitors Contribute to Blood Production under Native Conditions

Project description:The dynamics of the hematopoietic flux responsible for blood cell production in native conditions remains a matter of debate. Using CITE-seq analyses, we uncovered a distinct progenitor population that displays a cell cycle gene signature similar to the one found in quiescent hematopoietic stem cells. We further determined that the CD62L marker can be used to phenotypically enrich this population in the Flt3+ multipotent progenitor (MPP4) compartment. Functional in vitro and in vivo analyses validated the heterogeneity of the MPP4 compartment and established the quiescent/slow-cycling properties of the CD62L– MPP4 cells. Furthermore, studies under native conditions revealed a novel hierarchical organization of the MPP compartments in which quiescent/slow-cycling MPP4 cells sustain a prolonged hematopoietic activity at steady state while giving rise to other lineage-biased MPP populations. Altogether, our data characterize a durable and productive quiescent/slow-cycling hematopoietic intermediary within the MPP4 compartment and highlight early paths of progenitor differentiation during unperturbed hematopoiesis.

2023-10-23 | GSE243197 | GEO

Cell growth in aggregates determines gene expression, proliferation, survival and chemoresistance of Follicular Lymphoma

Project description:This SuperSeries is composed of the following subset Series: GSE41851: Expression data from follicular lymphoma cells cultured either in suspension either as Multicellular aggregates of lymphoma cells (MALC) GSE41855: Expression data from quiescent cells and cycling cells isolated from Multicellular aggregates of lymphoma cells (MALC) Refer to individual Series

2012-10-27 | E-GEOD-41856 | biostudies-arrayexpress

PROX1 mediates chemoresistance-associated recurrence via maintenance of quiescent colon cancer stem cells

Project description:Cancer stem cells (CSCs) are profoundly associated with refractory nature of cancer. A quiescent population of CSCs is responsible for tumorigenesis and chemoresistance in leukemia, whereas neither the presence nor clinical importance of the quiescent CSCs is clearly established in solid tumors. In colon cancer, LGR5 is regarded as a functional marker of CSCs, but heterogeneity among LGR5+ cells was not clearly defined. Here we stratified LGR5+ cells by single-cell gene expression analyses and revealed that a tumorigenic population of mouse LGR5+ cells resides in a quiescent state. We identified 23 signature genes that were uniquely expressed in the quiescent CSCs of mouse tumors, and found that 7 of them were also specifically expressed in a quiescent population of LGR5+ cells in human colon xenograft tumors. Among them, PROX1 was expressed in invasive fronts of colon tumors. PROX1 was induced by TCF1 (TCF7), and the TCF1-mediated PROX1 expression was responsible for not only the maintenance of quiescence but also chemoresistance of colon cancer organoids. Knockout of PROX1 in patient-derived xenograft tumors resulted in inhibition of tumor recurrence after chemotherapeutic treatment. Our data underscore the therapeutic importance of a quiescent CSC population in colon cancer.

2019-11-30 | GSE141157 | GEO

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