Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of Tcf7l2 Knockout in the development and identity of Mouse brain Thalamus at embryonic stage E18.5 and P60

ABSTRACT: The thalamus of the brain acts as a relay station; taking inputs from several parts of the brain and then sending the information to the cortex and vice versa. It is also the structure know to affected in several brain developmental disorders such as schizophrenia, autism spectrum disorders, bipolar disorders etc. Upon in situ hybridisation one can visualise the expression of the transcription factor Tcf7l2 to be highest in prosomeric regions of the thalamus throughout development. With this information in mind we set out to find out, if the expression of Tcf7l2 is essential for the identity of the thalamic structure. Therefore, Tcf7l2 was knocked (KO) out using Cre+mice at embryonic stage E18.5 and postnatal adult stage P60. The E18.5 Tcf7l2 KO is a total knockout and the P60 Tcf7l2 KO is neuron-specific knockout. Total RNA was extracted and sent for sequencing using Illumina 2500. The data obtained was aligned by HISAT2 alignment tool, and the excon read counts were gathered using htseq counts, and expression normalization and differential gene expression was analysed using DESeq2.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Mus musculus

SUBMITTER: Marta Wisniewska

PROVIDER: E-MTAB-8755 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Cortical, hippocampal and thalamic whole genome transcriptome data from controls and G72 schizophrenia mice of both sexes

Project description:G72 transgenic (TG, transgenic mice carrying the G72/G30 locus) and wildtype (WT) mice with a CD1 background were used for transcriptome data acquisition. Importantly, three different brain regions, i.e., the retrosplenial cortex, the hippocampus and thalamus, of animals from both sexes were investigated. In total, eight WT control animals (four ♂, age: 23.14 ± 0.00 wks; four ♀, age: 23.46 ± 0.11 wks) and eight G72 transgenic mice (four ♂, age: 23.14 ± 0.00 wks; four ♀, age: 23.14 ± 0.00 wks) were used for dissection of the cortex, thalamus and hippocampus for subsequent transcriptome analysis. Our data allow new insight into relevant alterations in gene transcript levels in G72 mice and allow the reader/user to carry out additional complex analyses to characterize potential sex-, age- and brain-region-specific profiles in gene expression and related pathways. These analyses could trigger biomarker identification and drug research and development in schizophrenia research in the future.

2023-12-01 | E-MTAB-13547 | biostudies-arrayexpress

RNA-seq of mouse pancreatic pericytes from wild-type and Tcf7l2-mutated mice

Project description:To characterise their gene expression, wild type pancreatic pericytes were isolated based on the YFP-labeling from Nkx3.2-Cre;EYFP mice. As control, whole isolated islets were analysed.To identify Tcf7l2-depenedent genes, pancreatic pericytes were isolated from Nkx3.2-Cre;EYFP;Tcf7l2 flox/flox transgenic mice, and compared to wild type cells.

2017-12-14 | E-MTAB-5325 | biostudies-arrayexpress

Chromatin occupancy and target genes of TCF7L2 in hepatocytes

Project description:TCF7L2 regulates multiple metabolic pathways in hepatocytes through a transcriptional network involving HNF4M-NM-1 For the identification of Tcf7l2 target genes using a RNA-seq timecourse, and for identifying the binding sites of Tcf7l2 and Hnf4a, Tcf7l2 was silenced in rat H4IIE hepatocytes using siRNA for Tcf7l2 with a scrambled siRNA as control. Treatment times for RNA-seq samples were 3, 6, 9, 12, 15, 18, 48, and 96 hours, and for ChIP-seq samples 15 h. RNA-seq timecourse was performed in duplicate or triplicate, and the ChIP-seq in duplicate for Tcf7l2 and in singlicate for Hnf4a. The H4IIE-specific transcriptome was defined from an independent set of pooled 24 h siRNA treated samples (N=3 for siRNA for Tcf7l2 and N=3 for scrambled siRNA).

2014-11-24 | E-GEOD-53862 | biostudies-arrayexpress

Gene expression profiling of optic nerve from Tcf7l2 mutant and control mice

Project description:We performed gene expression pofiling of of optic nerve from Tcf7l2 mutant and control mice and identified significantly changed genes in mutant. RNA-seq of P12 optic nerve from control and mutant mice.

2016-02-19 | E-GEOD-65118 | biostudies-arrayexpress

Expression data from thalamus or parietal lobe of FFI patients and normal human.

Project description:Fatal familial insomnia (FFI) is a special subtype of genetic human prion diseases that is caused by the D178N mutation of the prion protein gene (PRNP). In this study, global expression patterns of the thalamus and parietal cortex from three patients with FFI were analyzed by Affymetrix Human Genome U133+ 2.0 chip. We used microarrays to detail the global gene expression in tissues from normal human and FFI patients thalamus, or parietal lobe. Tissues from normal human and FFI patients' thalamus, or parietal lobe were for RNA extraction and hybridization on Affymetrix microarrays.

2015-08-30 | E-GEOD-40562 | biostudies-arrayexpress

Expression/Transcription profiling by high throughput sequencing of TCF7L2 KD and control in INS1 832/13 cells

Project description:Genetic variants in TCF7L2 are the most highly associated variants with type 2 diabetes.We performed RNA_seq experiments on Control and Knockdown samples for 4 passages each. Library preparation was performed according to mRNA Sequening Sample Preparation Guide (illumina). Reagents were taken from the Illumina sample preparation kit v.2. Knockdown and control samples were sequenced together in one flowcell, 6 samples per lane. The aim of this study is to identify the downstream target genes that might the involvement of TCF7L2 in the development of type 2 diabetes. No technical replicate, 4 biological replicates.

2013-12-15 | E-MTAB-2034 | biostudies-arrayexpress

5-hydroxymethylcytosine (5hmC) methylation profiling of adult mouse brain and liver tissues (hMeDIP-seq)

Project description:5-hydroxymethylcytosine (5hmC) is the first oxidative product of the TET-mediated 5-methylcytosine (5mC) demethylation pathway. It is a key intermediate in cytosine demethylation, and have potential regulatory functions with emerging importance in mammalian biology. In this work, we used a chemical capture-based technique that coupled with next-generation sequencing to investigate the global 5hmC methylation in five brain subregions (cerebellum, cortex, hippocampus, hypothalamus and thalamus) and liver tissues from female and male adult mice. We also performed total RNA sequencing to study the association between 5hmC and gene expression. The enriched 5-hmC library was sequenced on a HiSeq2500 by paired-end sequencing with 100 bp read length.

2017-01-31 | E-MTAB-5167 | biostudies-arrayexpress

Expression profiling of adult mouse brain and liver tissues (RNA-seq)

Project description:We carried out total RNA sequencing on RNA extracted from 5 brain subregions (cerebellum, cortex, hippocampus, hypothalamus and thalamus) and liver tissues of wild-type mice at 3 months of age. In total, two female and two male mice were used to obtain biological replicates for appropriate statistical analysis. Not only is this dataset used to perform expression analysis between brain subregions and between brain and liver, it is also used in-conjunction with 5hmC-seq methylation profiles that we performed to study the association between 5hmC and gene expression. Stranded RNA-seq library was prepared and sequenced on a HiSeq2500 by single end sequencing with 100 bp read length.

2017-01-31 | E-MTAB-5166 | biostudies-arrayexpress

Altering cancer transcriptomes using epigenomic inhibitors [RNA-Seq]

Project description:We have compared the genome-wide effects on the transcriptome after treatment with ICG-001 (the specific CBP inhibitor) versus C646, a compound that competes with acetyl-coA for the Lys-coA binding pocket of both CBP and p300. We found that both drugs cause large-scale changes in the transcriptome of HCT116 colon cancer cells and PANC1 pancreatic cancer cells, and reverse some tumor-specific changes in gene expression. Interestingly, although the epigenetic inhibitors affect cell cycle pathways in both the colon and pancreatic cancer cell lines, the WNT signaling pathway was affected only in the colon cancer cells. Notably, WNT target genes were similarly down-regulated after treatment of HCT116 with C646 as with ICG-001. To identify genes affected by direct targeting of a component of the transcriptional complex implicated in WNT regulation, we used siRNAs to knockdown TCF7L2 in PANC1 cells. Cells were treated with control siRNAs or siRNAs specific for TCF7L2 and RNA was analyzed by RNA-seq.

2015-01-07 | E-GEOD-63776 | biostudies-arrayexpress

E-MTAB-8755

Project description:Effect of Tcf7l2 Knockout in the development and identity of Mouse brain Thalamus at embryonic stage E18.5 and P60

2020-07-20 | E-MTAB-8755 | ExpressionAtlas