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RNA-seq profiling of mouse transformed culture cells as Pax6 locus cell models

ABSTRACT: RNA-seq profiling of mouse transformed culture cells as Pax6 locus cell models

PROVIDER: PRJNA489869 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7807231.fastq.gz	Fastqsanger.gz
	SRR7807232.fastq.gz	Fastqsanger.gz
	SRR7807233.fastq.gz	Fastqsanger.gz
	SRR7807234.fastq.gz	Fastqsanger.gz
	SRR7807235.fastq.gz	Fastqsanger.gz

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RNA-seq profiling of mouse transformed culture cells as Pax6 locus cell models

Project description:Transcriptome profiling using RNA-seq of MV+, a mouse lens epithelium cell line expressing Pax6 and RAG renal adenocarcinoma cell line which does not express Pax6.

2018-10-18 | GSE119660 | GEO

Characterisation by Next generation Capture-C of Pax6 locus in a mouse cell line with bleomycin treatment to relieve topological stress

Project description:NG-Capture-C profiling of chromatin interactions (using DpnII 3C and Oligo nucleotide sequence capture followed by Next generation sequencing) of enhancers, promoters and CTCF/Rad21 binding sites throughout a ~600kb region of the mouse Pax6 locus in β-TC3 cells treated with alpha amanitin. β-TC3 cell are a mouse pancreatic β cell derived from mouse insulinoma.

2023-06-21 | GSE235335 | GEO

Characterisation by Next generation Capture-C of Pax6 locus in a mouse cell line with alpha amanatin treatment to inhibit transcription

2023-06-21 | GSE235334 | GEO

PAX6-WNK2 axis governs corneal epithelial homeostasis

Project description:PURPOSE. Limbal stem/progenitor cells (LSC) continuously proliferate and differentiate to replenish the corneal epithelium and play a vital role in corneal function and normal vision. Previous study revealed that Paired box 6 (PAX6) is a master transcription factor involved in determining the fate of corneal epithelial cells (CEC). However, the molecular events downstream of PAX6 remain largely unknown. In this study, we aimed to clarify the regulation network of PAX6 in driving CEC differentiation. METHODS. An air-liquid culture system was used to differentiate LSC into mature CEC. Specific targeting PAX6 short-hairpin shRNAs were used to knock down PAX6 in LSC. RNA-seq was used to analyze shPAX6-transfected CEC and CEC differentiation-associated genes to identify the potential downstream targets of PAX6. RNA-seq analysis, quantitative real-time PCR, and immunofluorescence staining were performed to clarify the function of WNK lysine deficient protein kinase 2 (WNK2), a downstream target of PAX6, and its relationship with corneal diseases. RESULTS. WNK2 expression increased during CEC differentiation and decreased upon PAX6 depletion. The distribution of WNK2 was specifically limited to the central corneal epithelium and suprabasal layer of the limbus. Knockdown of WNK2 impaired the expression of CEC-specific markers (KRT12, ALDH3A1, and CLU), disrupted the corneal differentiation process, and activated the terms of keratinization, inflammation, and cell proliferation, consistent with PAX6-depleted CEC and published microbial keratitis. Thus, aberrant expression of WNK2 was linked to corneal ulcers. CONCLUSIONS. As a downstream target of PAX6, WNK2 plays an essential role in corneal epithelial cell differentiation and maintenance of corneal homeostasis.

2024-10-30 | GSE272034 | GEO

RNA-seq analysis in Cornea epithelial cells (CECs), skin epithelial cells (SECs), LSCs after knocking down PAX6 (3-D shPAX6 LSCs) and SESCs transduced with PAX6(3-D PAX6+ SESCs) upon 3-D differentiation

Project description:Purpose: We find that Wnt7a-PAX6 axis determine corneal epithelial cell fate. To obtain global evidence for successful cell fate conversion, we performed gene expression profiling by RNA-seq on CECs, SECs, and LSCs after knocking down PAX6 and on SESCs transduced with PAX6 upon 3-D differentiation. Methods: Under 3-D culture condition, limbal stem cell (LSCs) can be differentiated to Cornea epithelial cells (CECs), and skin epithelial stem cells (SESCs) can be differentiated to skin epithelial cells (SECs). Total RNA was isolated from CECs, SECs, and LSCs after knocking down PAX6 (3-D shPAX6 LSCs) and on SESCs transduced with PAX6 (3-D PAX6+ SESCs) upon 3-D differentiation. Libraries were prepared following published standard protocol (Fox-Walsh K et al., 2011, genomics, 266-71). mRNA profiles were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000. Results: Following optimized decoding and mapping workfollow, we mapped about 5 million sequence reads to the human genome and identified more than 23659 transcripts per sample. Conclusions: Hierarchical clustering analysis of differentially expressed gene signatures revealed that the gene expression pattern of SESCs with PAX6 transduction was strikingly similar to that of CECs, whereas the profile of LSCs with PAX6 knockdown was highly related to that in SECs upon differentiation. These data therefore provided global evidence for a decisive role of the WNT7A/PAX6 axis in cell fate conversion from SESCs to CECs. RNA-seq on CECs, SECs, and LSCs after knocking down PAX6 and on SESCs transduced with PAX6 upon 3-D differentiation, using Illumina HiSeq 2000

2014-07-11 | E-GEOD-54322 | biostudies-arrayexpress

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Coop-Seq Analysis Demonstrates that Sox2 Evokes Latent Specificities in the DNA Recognition by Pax6

Project description:Sox2 and Pax6 co-regulate genes in neural lineages and the eye by forming a ternary complex likely facilitated allosterically through DNA. We used the quantitative and scalable Cooperativity-by-sequencing (Coop-seq) approach to interrogate Sox2/Pax6 dimerization on a DNA library where five positions of the Pax6 half site are randomized yielding 1024 cooperativity factors. Consensus positions normally required for the high-affinity DNA binding by Pax6 need to be mutated for effective dimerization with Sox2. Out of the five randomized bases, a 5’ thymidin is present in most of the top ranking elements. However, according to structural models, this thymidin maps to a spacer region separating Sox and Pax half –sites and is not expected to directly interact with the binding proteins. Cooperative binding to the Coop-seq defined sequence signature was validated by classical EMSAs. Re-analysis of ChiPseq data identified several candidate elements in genomic regions co-bound by Sox2 and Pax6. A highly conserved Sox2/Pax6 bound site near the Sprouty2 locus consists of a prototype cooperativity signature. This element was verified to promote cooperative dimerization designating Sprouty2 as candidate target of Sox2/Pax6 in several mouse and human tissues including the brain and the eye. Collectively, the functional interplay of Sox2 and Pax6 demands the relaxation of high affinity binding sites and is enabled by alternative DNA sequences. We conclude that this binding mode evolved to warrant that a subset of target genes is only regulated in the presence of suitable partner factors.

2017-11-15 | GSE101529 | GEO

Characterisation by Next generation Capture-C of Pax6 locus in three mouse cell lines (MV+, RAG and β-TC3 cells).

Project description:NG-Capture-C profiling of chromatin interactions (using DpnII 3C and Oligo nucleotide sequence capture followed by Next generation sequencing) of enhancers, promoters and CTCF/Rad21 binding sites throughout a ~600kb region of the mouse Pax6 locus in three expression states, High (β-TC3), On (MV+) and OFF (RAG). β-TC3 cell are a mouse pancreatic β cell derived from mouse insulinoma, MV+ a lens epithelium cell line and RAG a mouse kidney adenocarcinoma cell line.

2018-10-18 | GSE120666 | GEO

ChIP-Chip tiling array for Rad21 in RAG cells (renal adenocarcinoma) over mouse Pax6 gene region. Agilent ChIP-chip, Agilent 4x180K.

Project description:Rad21 ChIP-ChIP in renal adenocarcinoma RAG cells, using custom tilling array covering Pax6 mm9 (Chr2:103500000-107499954) mm9. This study is part of a large data set study gene regulotry mechnism in the Pax6 locus and complements other ChIP-ChIP data.

2018-10-18 | GSE120665 | GEO

Pax6 mutant neocortex vs. wild type

Project description:Pax6 is a transcription factor with key functional roles in embryonic development. In order to identify downstream effectors of Pax6 in the developing cerebral cortex we performed microarray analysis. We compared gene expression profiles of cortical tissues isolated from wild type and Pax6-/- mouse embryos. In order to identify Pax6 downstream targets we carried out microarray analysis of Pax6-/- mutant mice. Pax6 is highly expressed in the mouse cerebral cortex at embryonic day E14.5, therefore we selected this tissue in order to compare gene expression profiles between wild type and Pax6-/- homozygous cortici. RNA samples were isolated from three mutant and three wild type embryos.

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