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Next Generation Sequencing analysis of Lhx6 heterozygote and null forebrain transcriptomes at post natal day 15

ABSTRACT: Next Generation Sequencing analysis of Lhx6 heterozygote and null forebrain transcriptomes at post natal day 15

PROVIDER: PRJNA422615 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6381391.fastq.gz	Fastqsanger.gz
	SRR6381392.fastq.gz	Fastqsanger.gz
	SRR6381393.fastq.gz	Fastqsanger.gz
	SRR6381394.fastq.gz	Fastqsanger.gz
	SRR6381395.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing analysis of Lhx6 heterozygote and null forebrain transcriptomes at post natal day 15

Project description:Here we characterize the changes in the forebrain transcriptome resulting from the deletion of the transcription factor Lhx6, generated by RNA-seq technology with biologic replication. Lhx6 is an essential regulatory gene in the development of cortical interneurons generated in the medial ganglionic eminences of the embryonic brain. This data contains insights into gene networks important for the development of medial ganglionic eminence derived interneurons.

2017-12-16 | GSE108161 | GEO

INCLUDE: Down syndrome early post-natal basal forebrain multiome

Project description:INCLUDE: Down syndrome early post-natal basal forebrain multiome

| PRJNA1276165 | ENA

INCLUDE: Down syndrome early post-natal basal forebrain multiome

Project description:INCLUDE: Down syndrome early post-natal basal forebrain multiome

| PRJNA1276164 | ENA

Comparison of gene expression signature between nascent Lhx6-GFP+ cells from mouse embryonic brain and differentiated Lhx6-GFP+ cells from ES cells (as well as comparing those of Lhx6-GFP+ and Lhx6-GFP- cells from ES cells)

Project description:There was a remarkable similarity in the molecular properties of the MGE-GFP+ and ES-GFP+ cells. In particular, genes that are important for medial ganglionic eminence (MGE) and cortical interneurons development are both high in expression in both MGE-Lhx6-GFP+ and ES-Lhx6-GFP+ cells (compared to ES-Lhx6-GFP- cells). To investigate how closely ES cells-derived Lhx6-GFP+ cells resembled authentic Lhx6+ MGE cells, and to define the molecular properties of the Lhx6-GFP+ and Lhx6-GFP- cells from differentiated ES cells, we compared their gene expression profiles. We used FACS to purify GFP+ cells from the E12.5 MGE of Lhx6-GFP transgenic mice. ES-Lhx6-GFP+ cells and ES-Lhx6-GFP- cells (both from D12 EB aggregates) were also isolated by fluorescent activated cell sorting (FACS) and all of the RNA samples were subjected to RNA expression microarray analyses.

2013-01-16 | E-GEOD-43508 | biostudies-arrayexpress

2013-01-16 | GSE43508 | GEO

Development of LHX6-inducible system in PK-1 and PK-9 cells

Project description:Epigenetic gene silencing by aberrant DNA methylation leads to loss of key cellular pathways in tumorigenesis. DNA methylation-mediated silenced genes in pancreatic cancer were searched by methyl-CpG targeted transcriptional activation (MeTA) method and LHX6 (LIM homeobox 6), a transcription factor involved in embryogenesis and head development, was selected as one of candidate genes. LHX6 was downregulated in most pancreatic cancer cell lines (83%: 10/12) mainly through promoter hypermethylation and histone deacetylation. Furthermore, LHX6 was also methylated in primary pancreatic cancers in a tumor-specific manner (57%: 16/28). In order to assess the biological significance of LHX6 in pancreatic tumorigenesis, we first performed colony formation assay and found that LHX6 re-expression inhibited colony formation in pancreatic cancer cell lines. Similarly, inducible expression of LHX6 inhibited cell proliferation and migration in LHX6 low-expressing pancreatic cancer cell lines. On the other hand, knockdown of LHX6 accelerated cell proliferation in LHX6 high-expressing pancreatic cancer cell lines. Our present results suggest that epigenetic inactivation of LHX6 plays an important role in pancreatic tumorigenesis by promoting cell proliferation.

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MTG8 interacts with LHX6 to specify cortical interneuron subtype identity

Project description:In the study we compared migrating embryonic cortical interneurons from control mouse embryos and ones carryng homozygous deletions of either Mtg8 or Lhx6. The aim was to identify genes that are co-regulated by LHX6 and MTG8.

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Next-generation sequencing facilitates quantitative analysis of control and Lhx6-/- molar 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 molar transcriptome profiling (RNA-seq) between control and Lhx6-/- mice to identify the potential target of Lhx6.

2020-08-14 | GSE156235 | GEO

Induction of human SST and PV neurons by expressing a single transcription factor LHX6

Project description:To systematically explore the effect of LHX6 on neural development and differentiation, we performed RNA-sequencing (RNA-seq) of hPSC-derived GINs at day 50 in vitro.RNAseq results could also confirm alteration of GINs identity with the overexpression of LHX6.

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Gene expression in E10.5 Maxillary Arch Mesenchyme from control and Lhx6-/-;Lhx8-/- mutant embryos

Project description:We used laser capture microdissection to isolate maxillary arch mesenchyme from E10.5 embryos. This tissue was collected from both control (3x) and Lhx6-/-;Lhx8-/- mutant (3x) samples. Transcriptional profiling was performed using Affymetrix GeneChip Mouse Genome 430 2.0 arrays. The mutant mice are of mixed genetic background of C57BL/6J, 129 and CD-1 strains. The head of E10.5 embryos was collected and embedded in Optimal Cutting Temperature resin (Tissue-Tek) by flash freezing on dry ice. The frozen sections were collected on polyethylene naphthalate membrane slides (Leica). Leica LMD6000 Laser Micro-Dissection System was used to cut out the normal expression domain of Lhx6 and Lhx8 in the maxillary arch mesenchyme. The tissue was collected from the entire antero-posterior extent of the maxillary arches. Total RNA was extracted using RNeasy Micro Kit (Qiagen). Subsequent steps of transcriptional profiling were performed by the New York University Genome Technology Center, beginning with the amplification of RNA by Ovation Nano Amplification system (NuGen). RNA samples from three wild-type and three Lhx6−/−;Lhx8−/− mutant embryos, all somite count- and sex-matched (females), were analyzed with Affymetrix GeneChip Mouse Genome 430 2.0 arrays. A list of Lhx-regulated genes were generated from the microarray result based on the following criteria: fold change in the average expression between wild types and Lhx6−/−;Lhx8−/− mutants is >1.5, the difference is statistically significant (P < 0.05) and the average intensity of the probe signal is >100 for wild-type and/or mutant samples. The resulting list of 212 genes was used for a gene ontology analysis with DAVID (27,28).

2015-07-23 | E-GEOD-71285 | biostudies-arrayexpress

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