Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomes Analysis of 4NQO induced-esophageal tumors of Wild Type and S100A14 CKO mice

ABSTRACT: Transcriptomes Analysis of 4NQO induced-esophageal tumors of Wild Type and S100A14 CKO mice

PROVIDER: PRJNA826519 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR18746566_1.fastq.gz	Fastqsanger.gz
	SRR18746566_2.fastq.gz	Fastqsanger.gz
	SRR18746567_1.fastq.gz	Fastqsanger.gz
	SRR18746567_2.fastq.gz	Fastqsanger.gz
	SRR18746568_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Transcriptomes Analysis of 4NQO induced-esophageal tumors of Wild Type and S100A14 CKO mice

Project description:Purpose: To fully realize the potential molecular mechanism that S100A14 deficiency enhances esophageal carcinogenesis Methods: Total RNA of esophageal tumors in 4NQO WT and 4NQO S100A 14 CKO group mice was extracted with TRIzol Reagent. RNA libraries were constructed using an Illumina TruSeq RNA Sample Preparation kit according to the manufacturer’s protocol. A total of 150 base paired-end reads were sequenced using the Novaseq 6000 S4 platform. The read alignment was conducted using TopHat 2.0.13, and relative transcript abundances and differentially expressed genes were determined using the DESeq R package. Results: We identified 14,157 transcripts in esophageal tumors of 4NQO WT and 4NQO S100A14 CKO group mice. Approximately 8% of the transcripts showed differential expression between the esophageal tumors of 4NQO WT and 4NQO S100A 14 CKO group mice, with a fold change ≥1.0 and p value <0.05. Conclusions: Our study represents the first analysis of esophageal tumors derived from S100A14 CKO mice with biologic replicates, generated by RNA-seq.

2022-07-07 | GSE200772 | GEO

Next Generation Sequencing of Wild Type and PTPRO-/- ESCC tumoral Transcriptomes

Project description:To induce tumorigenesis in the esophagus, 100 mg/mL of the water-soluble carcinogen 4NQO (Sigma-Aldrich) was added to the drinking water of 6-week-old mice for 16 weeks. The mice were sacrificed when body weight loss >1/3; otherwise, they were sacrificed 12 weeks after completion of 4NQO treatment.Total RNA from murine esophageal squamous cell carcinoma (Ptpro-/- vs. Ptpro+/+, N=3/group) was extracted and purified, transcriptome profiles were generated by deep sequencing, using Illumina HiSeq 2500 sequencer.

2018-10-02 | GSE120688 | GEO

4NQO treatment may modulate gene expression in mouse tongue

Project description:Determine whether 4NQO treatment may modulate gene expression in mouse tongue. C57BL/6J mice were given 4NQO (100ug/ml in drink) for 8 weeks; Non-treated control samples were used for comparison.

2016-05-24 | GSE75374 | GEO

Next Generation Sequencing of Ezh2-cKO and Utx cKO transcriptomes of exostoses in mice

Project description:Ezh2-cKO or Utx-cKO in chondrocytes initiate metachondromatosis which containing both exostoses and enchondromas. To figure out whether the exostoses of Ezh2-cKO and Utx-cKO were the similar tumore, we compared the transcriptional profiles using RNA-sequencing of exostoses from Ezh2-cKO and Utx-cKO mice.

2020-10-20 | GSE122089 | GEO

Tongue tissue gene profile in 4NQO induced tongue carcinogenesis before and after IL-1Ra interference

Project description:Nine groups of rat tongue tissue RNA samples, including three from normal control, three from 4NQO induced tongue tissue, and three from 4NQO induced and IL-1Ra interference tongue tissue (3 rats per group) were collected for gene microarray hybridization.

2017-02-11 | GSE42855 | GEO

Transcriptomic analysis of 4NQO-induced oral squamous cell carcinoma with agonistic anti-CD40 treatment

Project description:To investigate the anti-tumor effect of agonistic anti-CD40, 4NQO-indued OSCC mice with agonistic anti-CD40.

2023-10-23 | GSE217407 | GEO

Next-generation Sequencing Facilitates Quantitative Analysis of Wild Type and EED cKO mice Hippocampus Dentate Gyrus Transcriptomes

Project description:Purpose:Quantification differentially expressed genes and find target genes. The goals of this study are to compare Wild Type and EED cKO hippocampus dentate gyrus transcriptome profiling (RNA-seq) to quantitative reverse transcription polymerase chain reaction (qRT–PCR) differentially expressed genes and find target genes Methods: Hippocampus dentate gyrus mRNA profiles of 14-day-old wild-type (WT) and Embryonic Ectoderm Development conditional knockout (EED cKO) mice were generated by deep sequencing, in two biological replicates,using BGISEQ-500 platform.All RNA-Seq data were aligned to mouse genome version mm10 using HISAT.We use cluster software and Euclidean distance matrix for the hierarchical clustering analysis of the expressed gene and sample program at the same time, the clustering results can be viewed with javaTreeview. qRT–PCR validation was performed using SYBR Green assays. Results:Only transcripts that showed more than 2-fold differential expression compared to control were subjected to relevance network analysis. 1047 candidate genes that were differentially expressed with biological functional groups as compared between WT and EED cKO mice . Conclusions: Our study represents the first detailed analysis of Wild Type and EED cKO mice hippocampus dentate gyrus transcriptomes, with two biologic replicates, generated by RNA-seq technology.

2019-05-11 | GSE131035 | GEO

Migrating interneuron transcriptomes in Wt and CCP1 cKO mouse embryos

Project description:CCP1 is a deglutamylase responsible for protranslational modification of proteins. CCP1 cKO interneurons show impaired acto-myosin contraction and increased invasion of the cortex. Transcriptome analysis of Wt and cKO interneurones aimes at uncovering secondary disregulation of gene expression.

2018-02-22 | GSE104090 | GEO

ChIP-Seq for Yrr1 protein on Saccharomyces cerevisiae cells carrying different YRR1 alleles in response to 4-nitroquinoline-N-oxide (4NQO)

Project description:In this study, we constructed three isogenic strains of S96 yrr1Î background (its native YRR1 gene was knocked out) carrying three different YRR1 alleles, YRR1_S96, YRR1_YJM789, YRR1_S96-I775E, respectively. We then conducted chromatin immuno-precipitation followed by high-throughput sequencing (ChIP-Seq) for Yrr1 protein on the three strains grown in Yeast Peptone Dextrose medium (YPD) and YPD + 4NQO. ChIP-Seq for Yrr1 protein was performed in biological triplicates on S96 cells carrying three different YRR1 alleles grown in YPD and YPD + 4NQO. Immune-precipitated DNA were sequenced for all the three cultures and input genomic DNA was sequenced for one culture.

2015-12-04 | E-GEOD-74700 | biostudies-arrayexpress

PIK3CA and p53 mutations promote 4NQO-initated head and neck tumor progression and metastasis in mice

Project description:The effect of gain of function mutations in p53, pik3ca, and both genes in mouse tongue subject to 4NQO treatment on gene expression is characterized by RNASeq.

2022-04-19 | GSE143716 | GEO

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