Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sox2 suppresses gastric tumorigenesis in mice [RNA-seq]

ABSTRACT: Purpose: Sox2 expression marks gastric stem and progenitor cells, raising important questions regarding the genes regulated by Sox2 and the role of Sox2 itself during stomach homeostasis and disease. The goal of this study is to determine the function of and the genes regulated by Sox2 in the stomach. Methods: mRNA profiles of Sox2 WT and Sox2 KO gastric glands were generated by RNA-sequencing, in triplicate, using a Illumina HiSeq 2500 instrument, resulting in 36 million single-end 50bp reads per smaple. Sequencing reads were mapped to the mouse reference genome (mm10/GRCm38) using STAR (Dobin et al., 2013). Read counts over transcripts were calculated using HTSeq v.0.6.0 (Anders et al., 2015) based on a current Ensembl annotation file for mm10/GRCm38 (release 75). Results: Sox2 is dispensiable for gastric stem cell self-renewal and epithelial homeostasis, however modulates the expression of cancer and intestinal related genes.

ORGANISM(S): Mus musculus

PROVIDER: GSE83964 | GEO | 2016/08/04

SECONDARY ACCESSION(S): PRJNA327571

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Sox2 suppresses gastric tumorigenesis in mice [RNA-seq]

Project description:Purpose: Sox2 expression marks gastric stem and progenitor cells, raising important questions regarding the genes regulated by Sox2 and the role of Sox2 itself during stomach homeostasis and disease. The goal of this study is to determine the function of and the genes regulated by Sox2 in the stomach. Methods: mRNA profiles of Sox2 WT and Sox2 KO gastric glands were generated by RNA-sequencing, in triplicate, using a Illumina HiSeq 2500 instrument, resulting in 36 million single-end 50bp reads per smaple. Sequencing reads were mapped to the mouse reference genome (mm10/GRCm38) using STAR (Dobin et al., 2013). Read counts over transcripts were calculated using HTSeq v.0.6.0 (Anders et al., 2015) based on a current Ensembl annotation file for mm10/GRCm38 (release 75). Results: Sox2 is dispensiable for gastric stem cell self-renewal and epithelial homeostasis, however modulates the expression of cancer and intestinal related genes. mRNA profiles of stomachs from 10 week old Sox2 WT and Sox2 KO mice were generated by sequencing, in triplicate, using a Illumina HiSeq 2500.

2016-08-04 | E-GEOD-83964 | biostudies-arrayexpress

Sox2 suppresses gastric tumorigenesis in mice [CHIP-seq]

Project description:Purpose: Sox2 expression marks gastric stem and progenitor cells, raising important questions regarding the genes regulated by Sox2 and the role of Sox2 itself during stomach homeostasis and disease. The goal of this study is to determine the function of and the genes regulated by Sox2 in the stomach. Methods: Sox2 ChIP-enriched DNA and input DNA was isolated from gastric glands of adult antrum from Sox2 KO and Sox2 WT mice. DNA was purified and genomic libraries were prepared as described (Sulahian et al., 2014), using four micrograms of goat anti-SOX2 (AF2018, R&D). Libraries were sequenced (50 bp, single-end reads) on an Illumina Hi-Seq 2000 instrument. Results: Sox2 is dispensiable for gastric stem cell self-renewal and epithelial homeostasis, however modulates the expression of wnt, intestinal and cancer related genes

2016-08-04 | GSE83965 | GEO

Sox2 suppresses gastric tumorigenesis in mice [CHIP-seq]

Project description:Purpose: Sox2 expression marks gastric stem and progenitor cells, raising important questions regarding the genes regulated by Sox2 and the role of Sox2 itself during stomach homeostasis and disease. The goal of this study is to determine the function of and the genes regulated by Sox2 in the stomach. Methods: Sox2 ChIP-enriched DNA and input DNA was isolated from gastric glands of adult antrum from Sox2 KO and Sox2 WT mice. DNA was purified and genomic libraries were prepared as described (Sulahian et al., 2014), using four micrograms of goat anti-SOX2 (AF2018, R&D). Libraries were sequenced (50 bp, single-end reads) on an Illumina Hi-Seq 2000 instrument. Results: Sox2 is dispensiable for gastric stem cell self-renewal and epithelial homeostasis, however modulates the expression of wnt, intestinal and cancer related genes Examination of Sox2 targets in the stomachs of Sox2 WT and Sox2 KO mice.

2016-08-04 | E-GEOD-83965 | biostudies-arrayexpress

Effects of gene-by-environment interaction on the mRNA profile in the light of differential susceptibility

Project description:Purpose: Investigation of effects of early adversity in mice deficient for serotonin transporter on mRNA expression in the context of differential susceptibility Methods: Following prenatal stress and behavioural screening in adulthood, month old females, either wildtype or carrying a heterozygous knockout of the serotonin transporter gene, were sacrificed, brains extracted, the hippocampi of both hemispheres dissected, blended and separated in two protions. From one of these portions RNA was extracted. Extracted RNA was further processed by an external company, i.e. IGA Technologies (Udine, Italy). Following library preparation, samples were sequenced on the illumina HiSeq2000 platform (single end, 50 bp, 30 million reads/sample). Reads were mapped to the Mus musculus GRCm38.p5 genome using STAR (Dobin et al. 2013). Following mapping, the reads per position were determined using HTSeq (Anders et al. 2015). These counts were then used for the analysis of differentially expressed genes (DEGs) using the R package DeSeq2 (Love et al. 2014). Results: dependent on the serotonin transporter genotype and behaviourally determined susceptibility to early life adversity, animals displayed distinct gene expression. As expected, the effect sizes and significances were rather subtle. Conclusion: the modulation of differential susceptibility seems to be modulated by distinct mRNA expression profiles, dependent on the serotonin transporter genotype

2024-01-27 | GSE109929 | GEO

Quantitative Analysis of hippocampal transcriptomes form wild-type, control and Kdm5c mutant mice (KO and ifKO) through Next Generation Sequencing (RNA-Seq)

Project description:RNA preparation for sequencing was performed as described in (Fiorenza et al., 2016). Hippocampi derived from three different animals were pooled together for each sample and three independent samples were sequenced. RNA-seq datasets from Kdm5c null mice and control littermates at their home cages (HC) and after 1 h of novelty exploration (NE) were generated by next-generation sequencing (RNA-seq) using Illumina HiSeq 2500 apparatus, where the configuration was in conditional samples paired-end and in conventional samples single-end. RNA-Seq libraries were prepared from total RNA using poly(A) enrichment of the mRNA (mRNA-Seq). The libraries were stranded and multiplexed. Quality control of the raw data was performed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Library sizes can be found in Suppl Table 9 of the manuscript. RNA-Seq libraries were mapped to reference genome (Ensembl GRCm38) using STAR v2.5.0c (Dobin A. et al. 2013), and with corresponding gene model annotation (Mus_musculus.GRCm38.83.gtf). Samtools (v1.3) was used to further process BAM files (Li et al., 2009). For calling of differentially expressed genes (DEG), mapped reads were counted with HTSeq v0.6.1 (Anders et al., 2014) at gene level and count tables were analysed using DeSeq2 (v1.10.0) R-package (Love et al., 2014) and bioconductor v3.2. For consideration of differentially regulated genes between conditions, we used adjusted p-value < 0.1 as indicated in the manuscript.

2017-08-18 | GSE85874 | GEO

CARD9-associated Dectin-1 and Dectin-2 are Required for Protective Immunity of a Multivalent Vaccine Against Coccidioides posadasii Infection

Project description:Preparation of sequencing libraries and sequencing analysis using Illumina HiSeq 3000 platform (50 bp single-read module) were conducted at the Genomics Core of UT Health San Antonio. Sequencing reads were preprocessed by Trim Sequences tools in CLC Genomics workbench. Remaining reads were then aligned to mouse GRCm38(mm10) reference genome using RNA-Seq Analysis module in CLC Genomics workbench. To determine differentially expressed genes, exact test were performed after filtering lowly expressed gene (counts per million < 1 in more than three samples across the dataset) using edgeR package (Robinson, McCarthy et al. 2010). Gene Ontology (GO) analysis were performed using DAVID (Dennis, Sherman et al. 2003) and then visualized by GOplot (Walter, Sanchez-Cabo et al. 2015).

2020-04-16 | GSE133140 | GEO

Effects of gene-by-environment interaction on the transcriptome of mice deficient for tryptophan hydroxylase 2 [RNA-seq]

Project description:Purpose: Investigation of effects of early adversity in mice deficient for brain serotonin on the transcriptome Methods: Following materal separation in early childhood and behavioural screening in adulthood, 4 moth old males, either wildtype or carrying a hetero- or homozygous knockout of the thryptophan hyroxylase 2 gene, were sacrificed, brains extracted, the amygdalae of both hemispheres dissected, blended and separated in two protions. From one of these portions RNA was extracted. Extracted RNA was further processed by an external company, i.e. IGA Technologies (Udine, Italy). , library preparation was performed using TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, US) that captures coding RNA and multiple forms of non-coding RNA, with a total input of 300 ng of RNA, as measured with Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) following manufacturer’s recommendations. The sequencing was performed using the Illumina HiSeq 2500 platform at a read-length of 125 bp with paired end reads yielding 60 million reads/sample. Reads were mapped to the Mus musculus GRCm38.p5 genome using STAR (Dobin et al. 2013). Following mapping, the reads per position were determined using HTSeq (Anders et al. 2015). Results: Either Tph2 genotype, early adversity as well as their interaction resulted in unique profiles of differentially expressed RNA. As expected, the effect sizes and significances were rather subtle. Conclusion: Tph2, MS and their interaction induced changes in gene expression and DNA methylation, within a physiological range. The observed changes by MS seemed furthermore strongly influenced by the Tph2 genotype, ergo brain 5-HT availability.

2019-05-06 | GSE110328 | GEO

RNA-Seq analysis of the pancreatic islets from 6-week-old Paupar WT and KO mice

Project description:Transcriptional analysis of the pancreatic islets of adult Paupar KO mice versus Paupar WT mice. Total RNA from Paupar WT and Paupar KO mice was converted into cDNA libraries (TruSeq RNA sample preparation kit, Illumina) according to manufacturer’s instructions. Sequencing was performed to a depth of 30 million, single-end reads in three biological replicates per genotype. Reads were aligned to the mouse genome (mm9) using HISAT2 v2.1.0 (Kim et al., 2013). Aligned reads were assigned to genes using annotations from Ensembl (Mus_musculus.GRCm38.73.gtf) and HTseq-count v0.10.0 (Anders et al., 2015). Differential expression across cohorts was assessed using DESeq2 v1.18 (Love, Huber, and Anders, 2014). Among the downregulated genes with a p-value < 0.05 genes important for alpha cell identity and function.

2019-10-10 | GSE121884 | GEO

RNA-seq of 12-weeks-old male murine heart ventricles.

Project description:RNA-Seq analysis of mouse cardiac transcriptome. RNA was isolated from the ventricles of 12-weeks-old male mice. Sequencing libraries were prepared using TrueSeq Stranded RNA LT Kit Ribo-Zero Gold (Illumina, 15032619). Libraries were pair-end sequenced on a MiSeq sequencer (Illumina) and mapped to the Mus musculus reference genome GRCm38 (https://support.illumina.com/sequencing/sequencing_software/igenome.html) using TopHat2 (Kim et al., 2013). Differential gene-expression analysis between controls and the EphB4 flox mice was performed using DESeq2 (Love et al., 2014). Read counts were obtained with HTSeq (Anders et al., 2015). Genes were considered as differentially expressed when the FDR-adjusted p-value was Ôëñ0.05.

2020-01-15 | E-MTAB-7686 | biostudies-arrayexpress

Strand-oriented RNAseq of LNCaP prostate cancer cells in culture for 24h in the presence of androgen

Project description:The aim of this study was to use NGS RNAseq deep-sequencing in order to characterize the polyadenylated mRNAs and lncRNAs expressed in LNCaP cells treated with androgen hormone compared with untreated LNCaP cells (GSE79301). Trimmed reads were mapped using the hg19 genome with TopHat v.2.0.12 and Bowtie v.2.2.3. The assembly was guided by a custom GTF file created with transcripts fromhuman lncRNA annotations from GENCODE v19 (Harrow, Frankish et al.2012) and those already annotated as lincRNAs in (Cabili, Trapnell et al. 2011; Prensner, Iyer et al. 2011; Hangauer, Vaughn et al. 2013). The diferencial expression was calculated by the sum of exon read count per gene with HTSeq (Anders, Pyl et al. 2015), followed by a DESeq2 analysis (Love, Huber et al. 2014).

2017-12-31 | GSE102305 | 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