Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Pseudotime ordering of cell cycle state

ABSTRACT: We will be using G&T method to sequence single cell genome and transcriptome derived from FS13B iPSCs cell line. The cell cycle state of each of the single cells is known. Hence, we will be analysing the genome and transcriptome of single cells from each of the cell cycle state to generate a copy number profile and transcriptome profile per given cell cycle stage: G1, S, G2, S.

PROVIDER: EGAS00001003293 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

EGAS00001003293-sc-2020-01-29T09:22:41Z - samples

Project description:We will be using G&T method to sequence single cell genome and transcriptome derived from FS13B iPSCs cell line. The cell cycle state of each of the single cells is known. Hence, we will be analysing the genome and transcriptome of single cells from each of the cell cycle state to generate a copy number profile and transcriptome profile per given cell cycle stage: G1, S, G2, S. . This dataset contains all the data available for this study on 2020-01-29.

| EGAD00001005919 | EGA

Retinoic Acid Promotes Endothelial Cell Cycle Early G1 State to Enable Human Hemogenic Endothelial Cell Specification

Project description:Endothelial cells derived from hESCs were separated into 4 different cell cycle phases via FACS and sequenced (i.e., early G1, late G1, G1/S, S/G2/M)

2021-01-01 | GSE159694 | GEO

Leukemia reconstitution in vivo is driven by cells in early cell cycle and low metabolic state

Project description:To characterize LICs in ALL irrespective of surface markers expression, we investigated leukemia initiating activities of cellular subfractions of patient-derived xenograft BCP-ALL cells sorted according to different cell cycle phases (i.e. G0/G1 and G2/M) followed by transplantation onto NOD/SCID mice. All cell fractions led to leukemia engraftment indicating LIC activity irrespective of cell cycle stage. Most importantly, cells isolated from G0/G1 cell cycle phases led to early leukemia engraftment in contrast to cells from late cell cycle (G2/M). To further characterize cells with different engraftment potential in vivo, we analyzed the gene expression profiles of early (G1b early) and late (G2/M) engrafting cells.

2018-03-18 | GSE71836 | GEO

Cell cycle states of pluripotent cells dictate lineage decisions

Project description:Cell cycle and differentiation decisions are tightly linked; however, the underlying principles that drive these decisions are not fully understood. Here, we combined cell-cycle reporter system and single-cell RNA-seq profiling, to study the transcriptomes of mouse embryonic stem cells (ESCs) in the context of cell cycle states and differentiation. By applying a retinoic acid-based differentiation protocol we show that only cells in the G2/M phase are capable of differentiating into extraembryonic endoderm cells (XENs), whereas cells in the G1 phase predominantly produce epiblast stem cells (EpiSCs). Mechanistically, we show that Esrrb is a potent XEN state inducer as it is predominantly upregulated during G2/M phase, and cells engineered to overexpress Esrrb during G1 phase forced the cells to become XENs. Interestingly, this phenomenon is unique to the pluripotency ground state as sorting cells after 48 hours of differentiation resulted in a cell cycle-independent differentiation decisions. Cells in both G1 and G2/M phases contributed equally to EpiSC and XEN cellular lineages. Taken together, this study reveals an important functional link between cell-cycle states of pluripotent cells and lineage decisions, emphasizing the regulatory role of cell cycle during exit from pluripotency and can be further expand our understanding of early differentiation events.

2022-05-19 | GSE178390 | GEO

MiRNA signatures in cell cycle sorted cells [HeLa_H295R_miRNA_seq]

Project description:For the further examination of cell cycle dependent miRNA expression profile, DNA content based fluorescence activated cell sorting (cell cycle sort) was performed on human transformed cancer cell lines. Phase-dependent miRNA expression profiling was performed on G1, S and G2 phases. Results were validated by quantitative real-time PCR. Phase-dependent miRNA expression profiling was performed on sorted human cancer (cervical - HeLa, adrenocortical - NCI-H295R) cells). G1, S and G2 phases were successfully sorted and analyzed.

2016-05-28 | E-GEOD-73200 | biostudies-arrayexpress

Gene expression signatures in cell cycle sorted cells [HeLa_mRNA_array]

Project description:For the further examination of cell cycle dependent gene expression profile, DNA content based fluorescence activated cell sorting (cell cycle sort) was performed on human transformed cancer cell lines and primary, untransformed fibroblasts. Phase-dependent gene expression profiling was performed on G1, S and G2 phases. Results were validated by quantitative real-time PCR. Phase-dependent gene expression profiling was performed on sorted human cancer (cervical - HeLa and adrenocortical - NCI-H295R) cells and primary untransformed fibroblasts (HDFa). G1, S and G2 phases were successfully sorted and analyzed. HeLa_mRNA dataset

2016-05-28 | E-GEOD-73196 | biostudies-arrayexpress

Transcriptomic characterization of the human cell cycle in individual unsynchronized cells

Project description:Here, we profiled transcription across the cell cycle in single human myxoid liposarcoma cells, without prior synchronization. Flourescence-activated cell sorting was used to infer G1, S or G2/M cell cycle stages after staining cells for DNA content. Single-cell RNA-sequencing was performed according to the Smart-seq2 protocol.

2017-11-09 | E-MTAB-6142 | biostudies-arrayexpress

MiRNA signatures in cell cycle sorted cells [HeLa_H295R_miRNA_seq]

2016-05-28 | GSE73200 | GEO

MiRNA signatures in cell cycle sorted cells [H295R_miRNA_array]

Project description:For the further examination of cell cycle dependent miRNA expression profile, DNA content based fluorescence activated cell sorting (cell cycle sort) was performed on human transformed cancer cell lines and primary, untransformed fibroblasts. Phase-dependent miRNA expression profiling was performed on G1, S and G2 phases. Results were validated by quantitative real-time PCR.

2016-05-28 | GSE73258 | GEO

MiRNA signatures in cell cycle sorted cells [HDFa_miRNA_array]

Project description:For the further examination of cell cycle dependent miRNA expression profile, DNA content based fluorescence activated cell sorting (cell cycle sort) was performed on human transformed cancer cell lines and primary, untransformed fibroblasts. Phase-dependent miRNA expression profiling was performed on G1, S and G2 phases. Results were validated by quantitative real-time PCR.

2016-05-28 | GSE73257 | 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