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Unstranded RNA-seq profiling of cerebral cortices from Taf8-deleted and Taf8-intact mouse embryos

ABSTRACT: Taf8 was deleted in the mouse central nervous system using our Taf8 conditional allele. To determine transcriptional changes due to Ta8 deletion in the developing CNS, unstranded RNA sequencing was performed on cortices from Taf8 deleted embryos (E14.5 Taf8lox/–NesCreT/+p53–/–) and control embryos (E14.5 Taf8+/+NesCreT/+p53–/–).

ORGANISM(S): Mus musculus

PROVIDER: GSE198503 | GEO | 2022/03/12

REPOSITORIES: GEO

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Stranded RNA-seq profiling of cerebral cortices from Taf8-deleted and Taf8-intact mouse embryos

Project description:Taf8 was deleted in the mouse central nervous system using our Taf8 conditional allele. To determine transcriptional changes due to Ta8 deletion in the developing CNS, stranded RNA sequencing was performed on cortices from Taf8 deleted embryos (E14.5 Taf8lox/–NesCreT/+p53–/–) and control embryos (E14.5 Taf8+/+NesCreT/+p53–/–).

2022-03-12 | GSE198502 | GEO

Unstranded RNA-seq profiling of cerebral cortices from Taf8-deleted and Taf8-intact mouse embryos

Project description:Unstranded RNA-seq profiling of cerebral cortices from Taf8-deleted and Taf8-intact mouse embryos

| PRJNA815650 | ENA

RNA-seq expression profiling of cerebral cortices from Taf8 deleted and Taf8 intact mouse embryos

Project description:Mutations in genes encoding general transcription factors cause neurological disorders. Despite clinical prominence, the consequences of defects in the basal transcription machinery during brain development are unclear. We found that loss of the TATA-box binding protein associated factor TAF8, a component of the general transcription factor TFIID, in the developing central nervous system affected the expression of many, but notably not all genes. Taf8 deletion caused apoptosis, unexpectedly restricted to forebrain regions. Nuclear levels of the transcription factor p53 were elevated in the absence of TAF8, as were the mRNAs of the pro-apoptotic p53 target genes Noxa, Puma and Bax. The cell death in Taf8–/– forebrain regions was completely rescued by additional loss of p53, but Taf8–/–p53–/– brains failed to initiate a neuronal expression program. Taf8 deletion caused aberrant transcription of promoter regions and splicing anomalies. We propose that TAF8 supports the directionality of transcription and co-transcriptional splicing, and that failure of these processes causes p53- induced apoptosis of neuronal cells in the developing mouse embryo. Taf8 was deleted in the developing mouse central nervous system (CNS) using our Taf8 conditional allele. In the absence of global effects of loss of TAF8 on RNA levels, we determined effects on individual gene loci by RNA sequencing of cortices from Taf8 deleted (E14.5 Taf8lox/–NesCreT/+p53–/–) and control (E14.5 Taf8+/+NesCreT/+p53–/–) cortices. The p53-deficient background was used to avoid complications due to apoptosis, but prevented us from examining changes in p53-induced gene transcription.

2022-03-12 | GSE198505 | GEO

RNA-seq expression profiling of cerebral cortices from Taf8 deleted and Taf8 intact mouse embryos

Project description:RNA-seq expression profiling of cerebral cortices from Taf8 deleted and Taf8 intact mouse embryos

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Stranded RNA-seq profiling of cerebral cortices from Taf8-deleted and Taf8-intact mouse embryos

Project description:Stranded RNA-seq profiling of cerebral cortices from Taf8-deleted and Taf8-intact mouse embryos

| PRJNA815651 | ENA

Mouse E15.5 cortices: Snf2l Ex6 deleted mice versus wild type controls

Project description:Gene expression profiling of mouse cortices in which the experimental strain lacks Exon 6 of the Snf2l gene which encodes an ATP-binding motif that is critical for chromatin re-modeling Comparison of gene expression in E15.5 cortices of Snf2l-Ex6DEL mice versus wild type controls. Two samples of each strain were used, with one pair of samples utilized for two of the replicates (dye-flip), the second pair then used for the third replicate.

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Mouse E15.5 cortices: Snf2l Ex6 deleted mice versus wild type controls

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Transcriptional profiling of E14.5 control and Tbr2 fl/fl;Foxg1::Cre cortices

Project description:The abscence of TBR2 gene in human leads to microcephaly. This condition is mimicked by the specific ablation of the murine gene in developing cerebral cortex. Herein we compared gene expression in control and Tbr2 cKO in E14.5 cerebral cortices. This approach represents a useful tool to identify the molecular mechanisms at the basis of the phenotype.

2016-09-08 | GSE63619 | GEO

Transcriptional profiling of E14.5 control and Tbr2 fl/fl;Foxg1::Cre cortices

2016-09-08 | E-GEOD-63619 | biostudies-arrayexpress

Co-assembly of stranded and unstranded RNA-seq data improves coding and noncoding transcriptome maps

Project description:We want to develop transcriptome assembly pipeline that significantly improves the quality of the assemblies constructed using stranded and/or unstranded RNA-seq data. Transcriptome of mouse embryonic stem cells (mESC) were assembled using stranded and unstranded library generated by Illumina HiSeq 2000

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