Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing Analysis of Transcriptomes of the HEK293T-Cas9 cells transfected with plasmid containing programmed scaffold RNA

ABSTRACT: By performing RNA sequencing (RNA-seq) analysis on the HEK293T-Cas9 cells which transfected with plasmid containing programmed scaffold RNA for non-targeting or for targeting Hemoglobin subunit gamma-1 (HBG1) we want to investigate whether the scaffold RNA and the endogenous mRNA could be captured in regular reverse transcription reaction. RNA-seq analysis showed that we can capture the scaffold RNA together with the endogenous mRNA precisely.

ORGANISM(S): Homo sapiens

PROVIDER: GSE143880 | GEO | 2020/05/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Next Generation Sequencing Analysis of the single-cell Transcriptomes of the K562-Cas9 cell infected with lentiviral sgRNA library containing programmed scaffold RNA

Project description:By performing RNA sequencing (RNA-seq) analysis on the K562-Cas9 cells which infected with genome-scale lentiviral sgRNA library, we want to investigate whether our strategy can be applied in CRISPR screen with single cell transcriptomic readout. RNA-seq analysis showed that we can capture the scaffold RNA together with the endogenous mRNA precisely. The gene expression profile after genome perturbation can be easily identified together with the perturbation information in single experiment.We performed Single cell RNA-Seq by Smart-seq2/C1 platform for 73 cells. The gRNA scaffold was not detected in five cells, the numbers for these cells are NKC1.8, NKC1.11, NKC1.12, NKC1.27 and NKC1.37.

2023-04-10 | GSE144230 | GEO

An optimized microRNA scaffold increases shRNA processing and target knockdown

Project description:Two shRNAs were placed into expression vectors harboring mir30 microRNA scaffold and an optimized scaffold where the artificial restriction sights in mir30 have been removed. After infection and selection shRNA processing was assessed by small-RNA cloning. For both shRNAs, placement into the optimized scaffold resulted in a ~two-fold increase in processing (based on smallRNA levels). Purpose: Others have reported that the EcoRI site that was introduced to the mir30 scaffold results in decreased smallRNA processing and hence reduced target knockdown. We've developed an alternative scaffold (termed ultramir) where this site is removed. smallRNA cloning was used to determine if the movement of this sight resulted in an increase in shRNA processing. Method: Two shRNAs (one targeting Renilla Luciferase and one targeting Human RPA3) were cloned into the original mir30 cassette the ultramir cassette. Each of the 4 constructs were infected in duplicate at single copy into cells and the cells seltected unitil infection percentages reached >90% (the shRenilla hairpin was infected into HEK293T cells and the shRPA3 construts into the Gallus gallus cell line ERC. After selection smallRNA cloning was perfromed and the amount of smallRNAs corrresponding to the two shRNAs compared to the endogenous microRNA populatlon. Results: smallRNA levels of the two shRNAs doubled relative to the microRNA population when they were placed into the ultramir scaffold.

2014-11-24 | E-GEOD-62187 | biostudies-arrayexpress

Transcriptomic profiling of HBG gene expression in HEK293T cell line

Project description:Efficiency of HBG gene activation by the Cas12f/cgRNA system. In a doxycycline-inducible dCas12f-VPR knock-in (KI) HEK293T cell line, transiently transfected plasmids encoding U6, linear, and circular gRNAs targeting HBG1, and cgRNAs targeting mNeonGreen (negative control, NC) to activate HBG gene expression. RNA-seq analysis showed that cgRNAs exhibited increased efficiency in the target gene HBG1 and slight lower specificity when compared with U6 and linear gRNAs.

2024-03-12 | GSE261105 | GEO

Next Generation Sequencing Analysis of Transcriptomes of the HEK293T-Cas9 cells transfected with plasmid containing programmed scaffold RNA

Project description:Next Generation Sequencing Analysis of Transcriptomes of the HEK293T-Cas9 cells transfected with plasmid containing programmed scaffold RNA

| PRJNA601968 | ENA

Project description:RNA-seq targeting HBG1 and HBG2

| PRJNA1073711 | ENA

Lakshman scaffold

Project description:Lakshman Kund scaffold Metagenomic assembly

| PRJNA902919 | ENA

Comparative Analysis of Cas9 Activators Across Multiple Species

Project description:RNA-Seq after Cas9-gRNA transfection with different activators targeting HBG1

2016-04-26 | GSE80611 | GEO

Murine host body reactions to implanted scaffolds: non-coat polystyrene scaffold vs. collagen- or PMB-coated scaffold

Project description:This study investigated early host reactions to implanted materials to predict successful tissue regeneration with implant. Three kinds of scaffold, i.e., non-coat, collagen-coated, and PMB-coated porous polystylene scaffolds were implanted subcutaneously in mice dorsal area. Those scaffolds were used as bio-incomopatible materials, appropriate materials for tissue regeneration (bio active), and inappropriate to regenration (bio-inert) scaffolds. Seven days after implantation, scaffolds were explanted and total RNA was isolated from infiltrated host cells into scaffold by laser microdissection. Gene expressions of cells in collagen- and PMB-coated scaffold were normalized using results of non coat scaffold. Genes with more than 2-fold difference between collagen and PMB were picked up and narrowed to related keywords; inflammation, angiogenesis, wound healing, and mcrophage polarization. Among those genes, interluekin (IL)-1beta which promote both inflammation and wound healing was up-regulated in collagen-coated scaffold. On the other hand, IL-10 which suppress both inflammation and wound healing was up-regulated in PMB-coated scaffold. Angiogenesis-promoting genes were up-regulated and angiogenesis suppressve genes were suppressed in collagen. Up-regulation of IL-1b and the angiogenesis-relating genes inside the porous scaffolds are the possibly important factors for controlling tissue regeneration. Three-condition experiment, host cells infiltrated in non coat (reference), collagen-coated, and PMB-coated scaffolds. Two-microarray condition experiments, collagen vs. non coat and PMB coat vs. non coat. Hybridization: 2 replicates. Scanning: 3 replicates. Biological experiments: once.

2014-01-23 | E-GEOD-52053 | biostudies-arrayexpress

Cas9 gRNA engineering for selectable genome editing, activation and repression

Project description:RNA-Seq after Cas9-gRNA transfection with different length gRNAs we performed PolyA Selection and RNA-Seq on cells transfected with dCas9-VPR and a gRNA of each length (20nt, 16nt, or 14nt) targeting ACTC1, MIAT, or HBG1/2

2015-07-15 | E-GEOD-70694 | biostudies-arrayexpress

Murine host body reactions to implanted scaffolds: non-coat polystyrene scaffold vs. collagen- or PMB-coated scaffold

2014-01-23 | GSE52053 | GEO