Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

37 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic characterization of the human cell cycle in individual unsynchronized cells

ABSTRACT: 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.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Erik Larsson Lekholm

PROVIDER: E-MTAB-6142 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Transcriptomic Characterization of the Human Cell Cycle in Individual Unsynchronized Cells.

Karlsson Joakim J Kroneis Thomas T Jonasson Emma E Larsson Erik E Ståhlberg Anders A

Journal of molecular biology 20171016 24

The highly fine-tuned dynamics of cell cycle gene expression have been intensely studied for several decades. However, some previous observations may be difficult to fully decouple from artifacts induced by traditional cell synchronization procedures. In addition, bulk cell measurements may have disguised intricate details. Here, we address this by sorting and transcriptomic sequencing of single cells progressing through the cell cycle without prior synchronization. Genes and pathways with known ...[more]

PMID: 29045817

Similar Datasets

LINE-1 DNA methylation levels in DPPA3 KO overexpressing DPPA3 mutants

Project description:DPPA3 mutants were overexpressed using a doxycycline system to identify regions in DPPA3 necessary for DNA methylation maintenance suppression

2020-10-22 | E-MTAB-9653 | biostudies-arrayexpress

Amplicon bisulfite sequencing of LINE-1 elements in TET catalytic mutants and DPPA3 KO ESCs rescued by doxycylin induced overexpression

Project description:Tet1, Tet2 and Tet1/Tet2 catalytic mutants as well as DPPA3 KO ESCs harboring a doxycyclin inducible Dppa3 transgene were induced for several days to monitor LINE-1 methylation levels.

2020-10-23 | E-MTAB-9654 | biostudies-arrayexpress

Single-cell RNA sequencing of differentiating mESCs using Smart-seq3

Project description:We report dynamics of X-chromosome upregulation (XCU) along X-chromosome inactivation (XCI) in mESCs as they differentiate into EpiSCs. F1 hybrid C57BL6/J × CAST/EiJ male and female mESCs were adapted to 2i/LIF and female cells grown in serum/LIF conditions were differentiated using Fgf2 and Activin A for 1, 2, 4 and 7 days to induce random XCI. scRNA-seq was performed using the Smart-seq3 protocol, providing full-length coverage together with molecular counting using UMIs. Allelic resolution is achieved using strain-specific SNPs in the data. We reveal dynamic balancing of X alleles as cells undergo XCI to compensate dosage imbalances between sexes as well as between X and autosomes. Furthermore, we reveal that female naïve mESCs with two active X chromosomes lack XCU on both alleles which has major implications for reprogramming studies. Finally, we estimate allelic transcriptional burst kinetics from the data and find that progressively increased burst frequencies underlies the XCU process.

2022-02-14 | E-MTAB-9324 | biostudies-arrayexpress

Transposable element expression at unique loci in single cells with CELLO-seq

Project description:We introduce a novel method (CELLO-seq) for long-read RNA sequencing at single cell resolution. CELLO-seq allows for full-length RNA sequencing and enables measurement of allelic, isoform and Transposable Element (TE) expression at unique loci. We use CELLO-seq to assess the widespread expression of TEs in 2-cell mouse blastomeres as well as human induced pluripotent stem cells (hiPSCs). Across both species, old and young TEs showed evidence of locus-specific expression, with simulations demonstrating that only a small number of very young elements in the mouse could not be mapped back to with high confidence. Exploring the relationship between the expression of individual elements and putative regulators revealed surprising heterogeneity, with TEs within a class showing different patterns of correlation, suggesting distinct regulatory mechanisms. CELLO-seq thus represents a significant advance in the research of TEs, highlighting that studying TEs in single cells and at single loci resolution is necessary for understanding how such elements are regulated and for gaining insight into their role during development.

2020-10-01 | E-MTAB-9577 | biostudies-arrayexpress

Single nuclei sequencing of human and Mice HFrEF data (Heart Failure with reduced ejection fraction)

Project description:Here we provide snRNA-seq datasets from heart failure patients with reduced ejection fraction and snRNA-SEQ of the corresponding LAD mouse model (permanent ligation of the left anterior descending artery)

2023-08-20 | E-MTAB-13264 | biostudies-arrayexpress

Amplicons of a ND5 mRNA segment to detect m1A1374 levels in HEK pTRMT10C cells and control cells

Project description:This experiment was set up to assess the effect of TRMT10C overexpression on m1A methylation levels at position 1374 of the mitochondrial encoded ND5 mRNA. To investigate if TRMT10C is the writer enzyme for this m1A site, a cell system providing tetracycline-inducible TRMT10C expression was used (termed pTRMT10C cells). To control the effect of tetracycline itself, a corresponding control cell line without the tetracycline-inducible TRMT10C plasmid was used (termed Ctl cells). Method description: pTRMT10C and Ctl cells were incubated with three different concentrations of tetracycline (0 µg/mL, 0.1 µg/mL and 1 µg/mL) for 24 hours. The RNA was isolated using a Trizol-based protocol. Afterwards a Reverse transcription was performed with the RT SuperScript-IV (SS-IV) and a ND5 specific RT primer. Next, PCR was conducted to amplify the sequence around the m1A position. The amplicon is about 100 bp of length and was sequenced in an Illumina Sequencing MiSeq 2x75 PE run. For both cell lines the m1A analysis method was conducted with 4 biological replicates for each of the three tetracycline concenctraion.

2023-07-24 | E-MTAB-12038 | biostudies-arrayexpress

Multi-modal single-cell sequencing of differentiating mESCs using Smart-seq3 and scATAC-seq

Project description:We report dynamics of X-chromosome upregulation (XCU) along X-chromosome inactivation (XCI) in mESCs as they differentiate into EpiSCs. F1 hybrid C57BL6/J × CAST/EiJ male and female mESCs were grown in serum/LIF conditions were differentiated using Fgf2 and Activin A for 1, 2, 4 and 7 days to induce random XCI in female cells. Multi-modal single-cell sequencing was performed using scATAC on nuclei and Smart-seq3 to assay chromatin accessibility and poly-A+ RNA expression, respectively. Allelic resolution is achieved using strain-specific SNPs in the data. We reveal dynamic balancing of X alleles as cells undergo XCI to compensate dosage imbalances between sexes as well as between X and autosomes. Furthermore, we reveal that female naïve mESCs with two active X chromosomes lack XCU on both alleles which has major implications for reprogramming studies. Finally, we estimate allelic transcriptional burst kinetics from the data and find that progressively increased burst frequencies underlies the XCU process.

2022-02-14 | E-MTAB-10714 | biostudies-arrayexpress

ATAC-seq of human (Homo sapiens) and cynomolgus macaque (Macaca fascicularis) iPSC and iPSC-derived NPC cell lines

Project description:ATAC-seq samples from 2 species and 2 cell types were generated to study cis-regulatory element evolution. Briefly, previously generated urinary stem cell derived iPS-cells (Homo sapiens) of 2 human individuals and fibroblast derived cynomolgus macaque iPSCs (Macaca fascicularis) of 2 individuals (Geuder et al. 2021) were differentiated to neural progenitor cells via dual-SMAD inhibition as three-dimensional aggregation culture (Chambers et al. 2009; Ohnuki et al. 2014). The NPC lines were cultured in NPC proliferation medium and passaged 2 - 4 times until they were dissociated and subjected to ATAC-seq together with the respective iPSC clones. ATAC-seq libraries were generated using the Omni-ATAC protocol (Corces et al. 2017) with minor modifications.

2023-10-25 | E-MTAB-13373 | biostudies-arrayexpress

The atlas of the human hypertrophied heart reveals impaired cell communication

Project description:Pathological cardiac hypertrophy is a leading cause of heart failure. The understanding of disease mechanisms is primarily based on experimental models, but knowledge of the full repertoire of cardiac cells and their gene expression profiles in the human heart is missing. Here, using large-scale single-nucleus transcriptomes, we highlight the transcriptional response of cardiomyocytes to pressure overload in humans with stenosis of the aortic valve and disclose major alterations in cellular cross-talk. Cardiomyocytes showed a reduction of incoming connections with endothelial cells and fibroblasts. Particularly Eph receptor tyrosine kinases, including the predominant EPHB1 gene, were significantly down-regulated in cardiomyocytes of the hypertrophied heart. We compared 5 AS patients to healthy patients from the human heart cell ATLAS (https://www.heartcellatlas.org). This repository contains the processed files from the single nuclei RNA-SEQ.

2021-12-06 | E-MTAB-11268 | biostudies-arrayexpress

Single Nuclei Sequencing of old and young mice hearts under senolytica (Ageing impairs the neuro-vascular interface in the heart)

Project description:Aging is a major risk factor for impaired cardiovascular health. The aging myocardium is characterized by microcirculatory and diastolic dysfunction and increased susceptibility to arrhythmias. Nerves align with vessels during development. However, the impact of aging on the cardiac neuro-vascular interface is entirely unknown. Here, we report that aging reduces nerve density specifically in the left ventricle and dysregulates vascular-derived neuro-regulatory genes. Aging leads to a down-regulation of miR-145 and de-repression of the neuro-repulsive factor Semaphorin-3A. miR-145 deletion, which increased Sema3a expression, or endothelial Sema3a overexpression reduced axon density, thus mimicking the observed aged heart phenotype. Removal of senescent cells, which accumulated with chronological age in parallel to the decline in nerve density, rescued age-induced denervation, reduced Sema3a expression, preserved heart rate variability and reduced electrical instability. These data suggest that senescence-associated regulation of neuro-regulatory genes is associated with reduced nerve density and, thereby, contributes to age-associated cardiac dysfunction.

2023-07-05 | E-MTAB-13093 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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