Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of Wild Type, H-NS KO and cover mutated H-NS Transcriptomes

ABSTRACT: The goals of this study are to compare the difference transcriptome of Wild Type, H-NS KO and cover mutated H-NS by RNA-seq

ORGANISM(S): Escherichia coli K-12

PROVIDER: GSE169499 | GEO | 2021/03/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Analysis of Wild Type, H-NS KO and cover mutated H-NS Transcriptomes

Project description:Analysis of Wild Type, H-NS KO and cover mutated H-NS Transcriptomes

| PRJNA716815 | ENA

Quantitation the lysine 2-hydroxyisobutyrylation of H-NS in TmcA KO and YiaC KO E. coli strains using PRM

Project description:Quantitation the lysine 2-hydroxyisobutyrylation of H-NS in TmcA KO and YiaC KO E. coli strains using PRM. PRM was performed on an Orbitrap Q Exactive Plus mass spectrometer with an EASY-Spray source coupled to a Nano-LC system (EASY-nLC 1000, Thermo Fisher Scientific, Waltham, MA).

2021-03-21 | PXD024897 | iProX

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and NS-DADm mice myocardium Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived heart transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: myocardium mRNA profiles of 6-week-old wild-type (WT) and whole-body knock-in mutations in DADs of both NCOR and SMRT (NS-DADm) mice were generated by Agilent 2100 Bio analyzer. we filter the low quality reads (More than 20% of the bases qualities are lower than 10),reads with adaptors and reads with unknown bases (N bases more than 5%)to get the clean reads. Then we map those clean reads onto reference genome, followed with novel gene prediction, SNP &INDEL calling and gene splicing detection. Finally, we identify DEGs (differentially expressed genes) between samples and do clustering analysis andfunctional annotations Results: Using an optimized data analysis workflow, we find genes upregulated and enriched in NS-DADm myocardium that were consistent with HDAC3 inhibitor treated heart compared with WT Conclusions: Our study represents the first detailed analysis of genes expression in myocardium of HDAC3 enzymatic activity-dead NS-DADm mice

2020-12-15 | GSE163215 | GEO

Loss of Rab22a prevents Angiotensin II-induced Hypertension and vascular dysfunction by inhibiting AT1R recyling

Project description:The goals of this study is to compare the differently expressed genes in abdominal aorta of Rab22a KO mice and Rab22a WT mice with or without Angiotensin II treatment for 14 days at the concentration of 500ng/kg/min.The mice (n=20) were randomly divided into 4 groups:WT+AngII,WT+NS,KO+AngII,KO+NS (n = 5 for each group). Mice in WT+NS and KO+NS groups were infused with saline or 500 ng/kg/min of WT+AngII and KO+AngII respectively. Then the abdominal aorta were used to identify differentially expressed genes among different groups.

2021-01-10 | GSE164494 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type HCT116 and MTF1-KO HCT116 injected tumor Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to use RNA-seq to find differences between WT and MTF1-KO tumor in colorectal cancer Methods: HCT116 cells and MTF1-KO HCT116 cells were injected subcutaneously into the back of NSG mice at 2x106 cells/recipient , At day 24 after injection，Tumor tissue were isolated from infected recipients，and Total RNA was collected. Besides,about 5x106 cultured HCT116 cells and MTF1-KO HCT116 cells were collected for total RNA isolation ,and sent all of them for sequencing. Conclusions: Our study represents the transcriptome difference between WT HCT116 tumor and MTF1-KO HCT116 tumor has a very positive significance for the pathological process of colorectal cancer，especially for cell adhension

2022-12-15 | GSE190435 | GEO

Oral tongue cancer: p53 NS+ vs. p53 NS- tumor

Project description:Transcriptional profiling of squamous cell carcinoma of oral tongue, comparing p53 NS+ and p53 NS- tumors. Goal was to determine differentially expressed genes between them based on global gene expression.

2020-05-04 | GSE89146 | GEO

Differential gene expression in mACVR1 NS v wt-ACVR1 NS.

Project description:To study the effect of the ACVR1 G328V mutation in tumor neurospheres with a background of NRASV12 overexpression and p53 knockdown. The goal of this study was to identify differentially expressed genes between mACVR1 NS v wt-ACVR1 NS.

2020-04-16 | GSE148732 | GEO

Esophageal Squamous Cell Carcinoma tumors from Indian patients: nuclear-stabilized p53 (NS+) versus unstable p53 (NS-) protein

Project description:Transcriptional profiling of Esophageal Squamous Cell Carcinoma (ESCC) tumors comparing samples harbouring nuclear-stabilized p53 (NS+) versus unstable p53 (NS-) protein, determined through immunohistochemistry (IHC) staining of the tumor sections. The goal was to identify the genes that were differentially regulated between NS+ and NS- ESCC samples.

2024-03-29 | GSE218109 | GEO

Transcriptome analysis for KDM6A mutated urothelial bladder carcinoma and EZH2 inhibitor treated KDM6A mutated urothelial bladder carcinoma

Project description:Purpose: The goals of this study are to compare 1. The transcription profile in KDM6A wildtype and KDM6A mutated urothelial bladder carcinoma. 2. The transcriptional changes in KDM6A mutated urothelial bladder carcinoma upon EZH2 inhibitor treatment.

2017-03-01 | GSE92723 | GEO

RNA-seq to profile the H-NS transcriptome in EHEC O157:H7 strain EDL933

Project description:In order to define the role of H-NS in regulating gene transcription and further find out the biological significance of this protein in EHEC, we conducted RNA-seq and then analyzed the transcriptome data, using EHEC O157:H7 strain EDL933 and Δhns. A total of 983 genes were found to be regulated by H-NS. 213 and 770 genes exhibited lower and higher transcript levels in Δhns than in WT, respectively. For instance, chemotaxis and flagellar associated genes were down-regulated in Δhns. Besides, 34 genes on virulence plasmid pO157 were down-regulated by H-NS. The outcome of RNA-seq were verified by real time quantitative PCR. As reported in Salmonella Typhimurium, Δhns showed a growth deficiency and altered fitness. We first detected that both stx1 and stx2 in EDL933 were repressed by H-NS. Although no survival difference between EDL933 and Δhns was detected when phagocytized by macrophage, we characterized the higher ability of colonization and in consequence the higher virulence of Δhns to BALB/c mice by experimental analyses than those of WT, especially when intact commensal flora of mice existed. This might indeed help us understand the core role of H-NS in depth.

2016-12-31 | GSE73969 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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