Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Probing cell identity hierarchies by fate titration and collision during direct reprogramming [scRNA-Seq]

ABSTRACT: Collide-seq: A systematic comparison of how different reprogramming transcription factors achieve conversion as well as an in-depth analysis of how cells resolve the conflict when more than one fate is instructed.

ORGANISM(S): Mus musculus

PROVIDER: GSE211862 | GEO | 2022/09/16

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Probing cell identity hierarchies by fate titration and collision during direct reprogramming [Cut & Tag]

Project description:Collide-seq: A systematic comparison of how different reprogramming transcription factors achieve conversion as well as an in-depth analysis of how cells resolve the conflict when more than one fate is instructed.

2022-09-16 | GSE210181 | GEO

Probing cell identity hierarchies by fate titration and collision during direct reprogramming [scRNA-seq & scATAC-seq]

2022-09-16 | GSE211863 | GEO

Probing cell identity hierarchies by fate titration and collision during direct reprogramming

Project description: Not available

| S-SCDT-MSB-2022-11129 | biostudies-other

Probing cell identity hierarchies by fate titration and collision during direct reprogramming

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-09-16 | GSE211864 | GEO

RNA polymerase II collision interrupts convergent transcription (RNA-seq)

Project description:Anti-sense non-coding transcripts, genes-within-genes, and convergent gene pairs are prevalent among eukaryotes. The existence of such transcription units raises the question of what happens when RNA polymerase II (RNAPII) molecules collide head-to-head. Here we use a combination of biochemical and genetic approaches in yeast to show that polymerases transcribing opposite DNA strands cannot bypass each other. RNAPII stops, but does not dissociate upon head-to-head collision in vitro, suggesting that opposing polymerases represent insurmountable obstacles for each other. Head-to-head collision in vivo results in RNAPII stopping as well, and removal of collided RNAPII from the DNA template can be achieved via ubiquitylation-directed proteolysis. Indeed, in cells lacking efficient RNAPII poly-ubiquitylation, the half-life of collided polymerases increases, so that these can be detected between convergent genes by ChIP-Seq. These results provide new insight into fundamental mechanisms of gene traffic control, and point to an unexplored effect of anti-sense transcription on gene regulation via polymerase collision. Total RNA was extracted from WT or Elongin C deletion mutant (elc1M-bM-^HM-^F) cells and strand-specific RNA-Seq was performed. Three biological replicates were performed for WT and elc1M-bM-^HM-^F.

2012-11-30 | E-GEOD-38383 | biostudies-arrayexpress

RNA polymerase II collision interrupts convergent transcription (ChIP-seq)

Project description:Anti-sense non-coding transcripts, genes-within-genes, and convergent gene pairs are prevalent among eukaryotes. The existence of such transcription units raises the question of what happens when RNA polymerase II (RNAPII) molecules collide head-to-head. Here we use a combination of biochemical and genetic approaches in yeast to show that polymerases transcribing opposite DNA strands cannot bypass each other. RNAPII stops, but does not dissociate upon head-to-head collision in vitro, suggesting that opposing polymerases represent insurmountable obstacles for each other. Head-to-head collision in vivo results in RNAPII stopping as well, and removal of collided RNAPII from the DNA template can be achieved via ubiquitylation-directed proteolysis. Indeed, in cells lacking efficient RNAPII poly-ubiquitylation, the half-life of collided polymerases increases, so that these can be detected between convergent genes by ChIP-Seq. These results provide new insight into fundamental mechanisms of gene traffic control, and point to an unexplored effect of anti-sense transcription on gene regulation via polymerase collision. ChIP-Seq of RNA polymerase II was performed with WT and Elongain C deletion mutant (elc1M-bM-^HM-^F) cells. 4H8 antibody against the Rpb1 C-terminal domain was used for RNA polymerase II immunoprecipitation, whilst mouse IgG antibody was used for control immunoprecipitations. Two biological replicates were performed for both WT and elc1M-bM-^HM-^F.

2012-11-30 | E-GEOD-38382 | biostudies-arrayexpress

RNA polymerase II collision interrupts convergent transcription (RNA-seq)

2012-11-30 | GSE38383 | GEO

RNA polymerase II collision interrupts convergent transcription (ChIP-seq)

2012-11-30 | GSE38382 | GEO

Expression profiles of Drosophila melanogaster males with DX mothers and X-chromosomes that were subjected to male-limited evolution

Project description:Intralocus sexual conflict, where males and females have different fitness optima for the same trait, has been suggested to potentially be resolved by genomic imprinting, whereby expression in offspring is altered according to parent-of-origin. However, this idea has not yet been empirically tested. Here, we designed an experimental evolution protocol in Drosophila melanogaster which enabled us to look for imprinting effects on the X-chromosome. We enforced father-to-son transmission of the X-chromosome for many generations, and compared fitness and gene expression levels between control males, males with a control X-chromosome that had undergone one generation of father-son transmission (CDX), and males with an X-chromosome that had undergone many generations of father-son transmission (MLX). Although fitness differences were consistent with lowered fitness of males with a paternally inherited X-chromosome, expression differences suggested that this was due to deleterious maternal effects rather than imprinting. We conclude that imprinting is unlikely to resolve intralocus sexual conflict in Drosophila melanogaster. 18 samples were analyzed. There were 3 replicate populations within each of 3 treatments (Control, CDX, and MLX), and two males were analyzed from each population, for a total of 18 males.

2012-04-16 | E-GEOD-37325 | biostudies-arrayexpress

Direct measurement of glyconanoparticles and lectin interactions by isothermal titration calorimetry.

Project description: Not available

| S-EPMC3526666 | biostudies-literature