Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CRISPR activation enables high fidelity reprogramming into human pluripotent stem cells (bulk cells)

ABSTRACT: CRISPR activation enables high fidelity reprogramming into human pluripotent stem cells (bulk cells)

PROVIDER: PRJNA682166 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13182627_1.fastq.gz	Fastqsanger.gz
	SRR13182627_2.fastq.gz	Fastqsanger.gz
	SRR13182628_1.fastq.gz	Fastqsanger.gz
	SRR13182628_2.fastq.gz	Fastqsanger.gz
	SRR13182629_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 30

Similar Datasets

CRISPR activation enables high fidelity reprogramming into human pluripotent stem cells

Project description:CRISPR activation enables high fidelity reprogramming into human pluripotent stem cells

| PRJNA682159 | ENA

CRISPR activation enables high fidelity reprogramming into human pluripotent stem cells (single cells)

Project description:CRISPR activation enables high fidelity reprogramming into human pluripotent stem cells (single cells)

| PRJNA682165 | ENA

CRISPR activation enables high-fidelity reprogramming into human pluripotent stem cells.

Project description:Conventional reprogramming methods rely on the ectopic expression of transcription factors to reprogram somatic cells into induced pluripotent stem cells (iPSCs). The forced expression of transcription factors may lead to off-target gene activation and heterogeneous reprogramming, resulting in the emergence of alternative cell types and aberrant iPSCs. Activation of endogenous pluripotency factors by CRISPR activation (CRISPRa) can reduce this heterogeneity. Here, we describe a high-efficiency reprogramming of human somatic cells into iPSCs using optimized CRISPRa. Efficient reprogramming was dependent on the additional targeting of the embryo genome activation-enriched Alu-motif and the miR-302/367 locus. Single-cell transcriptome analysis revealed that the optimized CRISPRa reprogrammed cells more directly and specifically into the pluripotent state when compared to the conventional reprogramming method. These findings support the use of CRISPRa for high-quality pluripotent reprogramming of human cells.

| S-EPMC8828555 | biostudies-literature

CRISPR activation enables high fidelity reprogramming into human pluripotent stem cells (bulk cells)

Project description:Conventional reprogramming methods rely on the ectopic expression of transcription factors to reprogram somatic cells into induced pluripotent stem cells (iPSC). Forced expression of transcription factors might lead to off-target gene activation and heterogeneous reprogramming, resulting in the emergence of alternative cell types and aberrant iPSC. Activation of endogenous pluripotency factors by CRISPR activation (CRISPRa) can potentially reduce this heterogeneity. Here we describe a high efficiency reprogramming of human somatic cells into iPSC using optimized CRISPRa. Efficient reprogramming was dependent on the additional targeting of the embryo genome activation-enriched Alu-motif and the miR-302/367 locus. Single-cell transcriptome analysis revealed that the optimized CRISPRa reprogrammed cells with more directly and specifically into the pluripotent state when compared to the conventional reprogramming method. These findings support the use of CRISPRa for high quality reprogramming of human iPSC.

2021-12-23 | GSE162529 | GEO

CRISPR activation enables high fidelity reprogramming into human pluripotent stem cells

Project description:Conventional reprogramming methods rely on the ectopic expression of transcription factors to reprogram somatic cells into induced pluripotent stem cells (iPSC). Forced expression of transcription factors might lead to off-target gene activation and heterogeneous reprogramming, resulting in the emergence of alternative cell types and aberrant iPSC. Activation of endogenous pluripotency factors by CRISPR activation (CRISPRa) can potentially reduce this heterogeneity. Here we describe a high efficiency reprogramming of human somatic cells into iPSC using optimized CRISPRa. Efficient reprogramming was dependent on the additional targeting of the embryo genome activation-enriched Alu-motif and the miR-302/367 locus. Single-cell transcriptome analysis revealed that the optimized CRISPRa reprogrammed cells with more directly and specifically into the pluripotent state when compared to the conventional reprogramming method. These findings support the use of CRISPRa for high quality reprogramming of human iPSC. This SuperSeries is composed of the SubSeries listed below.

2021-12-23 | GSE162530 | GEO

CRISPR activation enables high fidelity reprogramming into human pluripotent stem cells (single cells)

Project description:Conventional reprogramming methods rely on the ectopic expression of transcription factors to reprogram somatic cells into induced pluripotent stem cells (iPSC). Forced expression of transcription factors might lead to off-target gene activation and heterogeneous reprogramming, resulting in the emergence of alternative cell types and aberrant iPSC. Activation of endogenous pluripotency factors by CRISPR activation (CRISPRa) can potentially reduce this heterogeneity. Here we describe a high efficiency reprogramming of human somatic cells into iPSC using optimized CRISPRa. Efficient reprogramming was dependent on the additional targeting of the embryo genome activation-enriched Alu-motif and the miR-302/367 locus. Single-cell transcriptome analysis revealed that the optimized CRISPRa reprogrammed cells with more directly and specifically into the pluripotent state when compared to the conventional reprogramming method. These findings support the use of CRISPRa for high quality reprogramming of human iPSC.

2021-12-23 | GSE162528 | GEO

The compact high-fidelity EbCas12a enables all-in-one AAV delivery system

Project description:The compact high-fidelity EbCas12a enables all-in-one AAV delivery system

| PRJNA991955 | ENA

Human pluripotent reprogramming with CRISPR activators.

Project description:CRISPR-Cas9-based gene activation (CRISPRa) is an attractive tool for cellular reprogramming applications due to its high multiplexing capacity and direct targeting of endogenous loci. Here we present the reprogramming of primary human skin fibroblasts into induced pluripotent stem cells (iPSCs) using CRISPRa, targeting endogenous OCT4, SOX2, KLF4, MYC, and LIN28A promoters. The low basal reprogramming efficiency can be improved by an order of magnitude by additionally targeting a conserved Alu-motif enriched near genes involved in embryo genome activation (EEA-motif). This effect is mediated in part by more efficient activation of NANOG and REX1. These data demonstrate that human somatic cells can be reprogrammed into iPSCs using only CRISPRa. Furthermore, the results unravel the involvement of EEA-motif-associated mechanisms in cellular reprogramming.

| S-EPMC6035213 | biostudies-literature

The compact high-fidelity EbCas12a enables all-in-one AAV delivery system

Project description:we characterized a novel compact Cas12a ortholog, EbCas12a, from the Erysipelotrichia bacterium with activities in mammalian cells. It is with the PAM sequence of 5’-TTTV-3’ (V=A, G, C) and the smallest size of ~3.47kb among reported Cas12a orthologs so far. Moreover, enhanced EbCas12a (enEbCas12a) was also developed to have comparable editing efficiency with higher specificity to AsCas12a and LbCas12a in mammalian cells. With the help of the compact enEbCas12a, all-in-one AAV delivery system with crRNA for Cas12a was developed for both in vitro and in vivo. Altogether, with the help of the novel smallest high fidelity enEbCas12a, this first case of the all-in-one AAV delivery for Cas12a could greatly boost future gene therapy and scientific research.

2023-07-10 | GSE236647 | GEO

Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification.

Project description:BACKGROUND:Next-generation-sequencing (NGS) technologies combined with a classic DNA barcoding approach have enabled fast and credible measurement for biodiversity of mixed environmental samples. However, the PCR amplification involved in nearly all existing NGS protocols inevitably introduces taxonomic biases. In the present study, we developed new Illumina pipelines without PCR amplifications to analyze terrestrial arthropod communities. RESULTS:Mitochondrial enrichment directly followed by Illumina shotgun sequencing, at an ultra-high sequence volume, enabled the recovery of Cytochrome c Oxidase subunit 1 (COI) barcode sequences, which allowed for the estimation of species composition at high fidelity for a terrestrial insect community. With 15.5 Gbp Illumina data, approximately 97% and 92% were detected out of the 37 input Operational Taxonomic Units (OTUs), whether the reference barcode library was used or not, respectively, while only 1 novel OTU was found for the latter. Additionally, relatively strong correlation between the sequencing volume and the total biomass was observed for species from the bulk sample, suggesting a potential solution to reveal relative abundance. CONCLUSIONS:The ability of the new Illumina PCR-free pipeline for DNA metabarcoding to detect small arthropod specimens and its tendency to avoid most, if not all, false positives suggests its great potential in biodiversity-related surveillance, such as in biomonitoring programs. However, further improvement for mitochondrial enrichment is likely needed for the application of the new pipeline in analyzing arthropod communities at higher diversity.

| S-EPMC3637469 | biostudies-literature

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