Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq analysis of transcriptomic changes in HS2 enhancer perturbed cells

ABSTRACT: RNA-seq analysis of transcriptomic changes in HS2 enhancer perturbed cells

PROVIDER: PRJNA546521 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR9203370.fastq.gz	Fastqsanger.gz
	SRR9203371.fastq.gz	Fastqsanger.gz
	SRR9203372.fastq.gz	Fastqsanger.gz
	SRR9203373.fastq.gz	Fastqsanger.gz
	SRR9203374.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 10

Similar Datasets

RNA-seq analysis of transcriptomic changes in HS2 enhancer perturbed cells

Project description:Tissue-specific gene expression requires coordinated control of gene-proximal and distal cis-regulatory elements (CREs), yet functional analysis of putative gene-distal CREs such as enhancers remains challenging. Here we describe enhanced CRISPR/dCas9-based epigenetic editing systems, enCRISPRa and enCRISPRi, for multiplexed analysis of enhancer function in situ and in vivo. Using dual effector proteins capable of re-writing enhancer-associated chromatin modifications, we show that enCRISPRa and enCRISPRi modulate gene transcription by remodeling local epigenetic landscapes at sgRNA-targeted enhancers and associated genes. Comparing with existing methods, our systems display more robust and specific perturbations of gene transcription with minimal off-targets. Allele-specific targeting of enCRISPRa to oncogenic TAL1 super-enhancer modulates TAL1 expression and cancer progression in xenotransplants. Furthermore, multiplexed perturbations of lineage-specific enhancers in an enCRISPRi knock-in mouse establish in vivo evidence for lineage-restricted requirement of developmentally regulated enhancers during hematopoietic lineage specification. Hence, enhanced CRSIPR epigenetic editing provides opportunities for interrogating enhancer function in development and disease.

2020-01-30 | GSE132213 | GEO

ATAC-seq analysis of HeLa stable cells expressing LAMPS targeting the HS2 enhancer

Project description:We describe that light-activated phase separation at the targeted HS2 enhancer increases chromatin accessibility

2023-03-16 | GSE180545 | GEO

The human β-globin enhancer LCR HS2 plays a role in forming a TAD by activating chromatin structure at neighboring CTCF sites

Project description:We propose that the HS2 has a role in forming a β-globin TAD by activating neighboring CTCF sites and the role is beyond typical enhancer activity.

2021-06-07 | GSE159130 | GEO

ChIP-seq analysis of cas9, HA, H3K4me, H3K4me2, H3K9me3, H3K27ac, CTCF, GATA1 and TAL1 in HS2 enhancer perturbed K562 cells or other leukemia cell lines

Project description:ChIP-seq analysis of cas9, HA, H3K4me, H3K4me2, H3K9me3, H3K27ac, CTCF, GATA1 and TAL1 in HS2 enhancer perturbed K562 cells or other leukemia cell lines

| PRJNA546522 | ENA

ATAC-seq analysis of HeLa stable cells expressing LAMPS targeting the HS2 enhancer

Project description:ATAC-seq analysis of HeLa stable cells expressing LAMPS targeting the HS2 enhancer

| PRJNA748683 | ENA

Transcriptomic changes in the pituitary when pituitary enhancer of the Nr5a1 gene is deleted

Project description:NR5A1 is expressed in the pituitary gonadotropes and regulates their functional differentiation. We have previously identified a pituitary-specific enhancer region located in the 6th intron of the Nr5a1 gene. In this study, deletion of the pituitary enhancer by genome editing abolished the expression of NR5A1 in the pituitary gland, confirming the functional importance of the enhancer. Transcriptomic changes in the enhancer-deleted mouse pituitary were revealed in both males and females.

2022-10-28 | GSE216468 | GEO

RNA-seq of Chlorella sp. HS2: Comparison between freshwater and marine conditions at exponential and stationary growth phases

Project description:Chlorella sp. HS2 is a halotolerant microalga exhibiting relatively high biomass productivity and substantially high lipid accumulation in marine growth media, which suggests this alga as an important crop for industrial algal cultivation systems. To determine pathways leading to HS2's acclimation responses to salt stress, we performed RNA-seq analysis with triplicated cultures grown in freshwater and marine media at both exponential and stationary growth phases. We then run de novo assembly to obtain HS2 transcriptome, which in turn was annotated and processed to extract dysregulated pathways. Results showed a large proportion of down-regulated genes, for instance photosynthesis and TCA pathways. Photosynthesis appeared, however, to recover at the stationary phase, while the general down-regulation pattern was maintained.

2020-03-12 | GSE146789 | GEO

Epigenetic enhancer changes during oncogenic transformation

Project description:Epigenetic enhancer changes during oncogenic transformation

| PRJNA393898 | ENA

Fusarium oxysporum strain:HS2

Project description:Fusarium oxysporum strain:HS2 Genome sequencing and assembly

| PRJNA810584 | ENA

Sodalis praecaptivus strain:HS2

Project description:Sodalis praecaptivus strain:HS2 Genome sequencing and assembly

| PRJNA275861 | ENA