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

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

PROVIDER: PRJNA494025 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7945090_1.fastq.gz	Fastqsanger.gz
	SRR7945090_2.fastq.gz	Fastqsanger.gz
	SRR7945100_1.fastq.gz	Fastqsanger.gz
	SRR7945100_2.fastq.gz	Fastqsanger.gz
	SRR7945091_1.fastq.gz	Fastqsanger.gz

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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.

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Characterisation of three mouse cell lines by ATAC-seq (MV+, RAG and β-TC3 cells).

Project description:Chromatin accessibility profiling using ATAC-seq to study and identify novel Cis-regulatory elements of MV+ a lens epithelium cell line, RAG a mouse kidney adenocarcinoma cell line and β-TC3 cell a mouse pancreatic β cell, derived from mouse insulinoma.

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ChIP-Chip tiling array for CTCF and Rad21 in mouse β-TC3 cells (pancreatic insulinoma) MV+ (lens epithelium) and RAG cells (renal adenocarcinoma) over panel of genes including Pax6, Sox2, Otx2, Sox9.

Project description:CTCF and Rad21 ChIP-ChIP in mouse pancretic cells, pancreatic β-TC3 cells, lens epithelium MV+ cells and renal adenocarcinoma RAG cells, using custom tilling array covering a 66 Mb region around Pax6 (Chr2:75,000,000-141,000,000) mm9. Additional loci and regions, Sox2 (chr3:32,000,000-37,000,000), Otx2 (chr14:48,500,000-50,500,000), Rax (chr18:65,500,000-68,000,000), Hba a-globin (chr11:32,050,000-32,450,000), Six3 (chr17:85,200,000-86,700,000), Sox1 (chr8:11,800,000-12,800,000), Mab21L2 (chr3:85,850,000-86,850,000), Bmp4 (chr14:46,500,000-47,500,000), NeuroD1 (chr2:79,050,000-79,600,000), Prox1 (chr1:191,700,000-192,700,000), Hmx1 (chr5:34,700,000-36,200,000), H19-Igf2 (chr7:149500000-150500000), Sox9 (chr11:110000000-116000000).

2018-10-18 | GSE119658 | GEO

Characterisation of three mouse cell lines by ATAC-seq (MV+, RAG and β-TC3 cells).

Project description:Characterisation of three mouse cell lines by ATAC-seq (MV+, RAG and β-TC3 cells).

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ChIP-Chip tiling array for H3k27ac in mouse MV+ (lens epithelium) and RAG cells ( renal adenocarcinoma) over panel of genes including Pax6, Sox2, Otx2, Sox9.

Project description:Enhancer identification using H3k27ac ChIP-ChIP in mouse MV+ and RAG, using custom tilling array covering a 66 Mb region around Pax6 (Chr2:75,000,000-141,000,000) mm9. Additional loci and regions, Sox2 (chr3:32,000,000-37,000,000), Otx2 (chr14:48,500,000-50,500,000), Rax (chr18:65,500,000-68,000,000), Hba a-globin (chr11:32,050,000-32,450,000), Six3 (chr17:85,200,000-86,700,000), Sox1 (chr8:11,800,000-12,800,000), Mab21L2 (chr3:85,850,000-86,850,000), Bmp4 (chr14:46,500,000-47,500,000), NeuroD1 (chr2:79,050,000-79,600,000), Prox1 (chr1:191,700,000-192,700,000), Hmx1 (chr5:34,700,000-36,200,000), H19-Igf2 (chr7:149500000-150500000), Sox9 (chr11:110000000-116000000).

2018-10-18 | GSE119659 | GEO

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.

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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

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 | GSE235334 | 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

ChIP-Chip tiling array for H3k27ac in mouse β-TC3 cells over panel of genes including Pax6, Sox2, Otx2, Sox9.

Project description:Enhancer identification using H3k27ac ChIP-ChIP in mouse β-TC3 cells, using custom tilling array covering a 66 Mb region around Pax6 (Chr2:75,000,000-141,000,000) mm9. Additional loci and regions, Sox2 (chr3:32,000,000-37,000,000), Otx2 (chr14:48,500,000-50,500,000), Rax (chr18:65,500,000-68,000,000), Hba a-globin (chr11:32,050,000-32,450,000), Six3 (chr17:85,200,000-86,700,000), Sox1 (chr8:11,800,000-12,800,000), Mab21L2 (chr3:85,850,000-86,850,000), Bmp4 (chr14:46,500,000-47,500,000), NeuroD1 (chr2:79,050,000-79,600,000), Prox1 (chr1:191,700,000-192,700,000), Hmx1 (chr5:34,700,000-36,200,000), H19-Igf2 (chr7:149500000-150500000), Sox9 (chr11:110000000-116000000).

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