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STAG proteins mediate heterochromatin organization to support translation and cell identity [UMI-4C]

ABSTRACT: STAG proteins mediate heterochromatin organization to support translation and cell identity [UMI-4C]

PROVIDER: PRJNA671632 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12888183.fastq.gz	Fastqsanger.gz
	SRR12888184.fastq.gz	Fastqsanger.gz
	SRR12888185.fastq.gz	Fastqsanger.gz
	SRR12888186.fastq.gz	Fastqsanger.gz
	SRR12888187.fastq.gz	Fastqsanger.gz

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UMI-4C for quantitative and targeted chromosomal contact profiling

Project description:We developed a targeted chromosome conformation capture (4C) approach that uses unique molecular identifiers (UMI) to derive high complexity quantitative chromosome contact profiles with controlled signal to noise ratios. We demonstrate that the method improves the sensitivity and specificity for detection of long-range chromosomal interactions, and that it allows the design of interaction screens with predictable statistical power. UMI-4C robustly quantifies contact intensity changes between cell types and conditions, opening the way toward incorporation of long-range interactions in quantitative models of gene regulation. We constructed UMI-4C profiles of 13 different genomic loci (viewpoints) in five different cell lines, in order to study the 3D chromatin contact maps of these selected loci. The coordinates for these viewpoints are: G1p1 chrX:48646542; baitG1_3_5kb chrX:48641393; bait_50kb chrX:48595987; bait_165kb chrX:48476525; ANK1 chr8:41654693; hbb_3HS chr11:5221346; hbb_HBB chr11:5248714; hbb_HBBP1_G1 chr11:5266532; HBB_HBE chr11:5292159; HBB_HS2 chr11:5301345; HBB_HS3 chr11:5306690; HBB_HS5 chr11:5313539; HBB_HBD chr11:5256597

2016-06-15 | E-GEOD-76763 | biostudies-arrayexpress

STAG proteins mediate heterochromatin organization to support translation and cell identity [RNA-Seq]

Project description:STAG proteins mediate heterochromatin organization to support translation and cell identity [RNA-Seq]

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STAG proteins mediate heterochromatin organization to support translation and cell identity [Iso-Seq]

Project description:STAG proteins mediate heterochromatin organization to support translation and cell identity [Iso-Seq]

| PRJNA673168 | ENA

UMI-4C for quantitative and targeted chromosomal contact profiling

2016-06-15 | GSE76763 | GEO

UMI-4C for quantitative and targeted chromosomal contact profiling

2016-09-23 | GSE87209 | GEO

STAG proteins mediate heterochromatin organization to support translation and cell identity [UMI-4C]

Project description:Abstract to be added later

2021-06-06 | GSE160015 | GEO

UMI-4C in control and Haster-deficient mouse livers

Project description:The HASTER promoter region is a cis-regulatory element that stabilizes the transcription of HNF1A, preventing silencing or overexpression. We have generated a mouse model where the promoter of Haster has been specifically deleted in liver (Haster loxP/loxP; AlbCre). In liver the prevailing consequence is upregulation of HNF1A. We performed UMI-4C experiments to assess how Haster inactivation remodel 3D chromatin interactions of the Hnf1a promoter using the Hnf1a promoter as viewpoint (V1, Hnf1a promoter upstream CTCF site viewpoint; V2, Hnf1a promoter VP).

2022-05-01 | E-MTAB-11472 | biostudies-arrayexpress

UMI-4C in control and HASTER-deficient EndoC-betaH3 cells overexpressing HNF1A

Project description:The HASTER promoter region is a cis-regulatory element that stabilizes the transcription HNF1A. If HASTER is deleted after beta cells have been formed and HNF1A is already stably expressed, HASTER is not required to maintain HNF1A activity, and is only required to provide negative feedback on HNF1A. HNF1A binding to the HASTER promoter mediates the repression of the HNF1A gene itself. To determine whether HNF1A binding to the HASTER promoter remodels 3D chromatin interactions of the HNF1A promoter, we performed UMI-4C experiments in wild type and HASTER-promoter KO EndoC-betaH3 cells with or without doxycycline-induced HNF1A overexpression using the HNF1A promoter as viewpoint.

2022-05-01 | E-MTAB-11473 | biostudies-arrayexpress

UMI-4C in control and Haster-deficient mouse livers

Project description:UMI-4C in control and Haster-deficient mouse livers

| PRJEB51135 | ENA

UMI-4C in wild-type and p63-null surface ectoderm cells

Project description:Purpose: Validate HiChIP-identified long-range chromatin interactions at the TFAP2C locus, in a viewpoint-specific manner. Methods: UMI-4C libraries targeting 3 individual viewpoints at the TFAP2C locus were generated in duplicate, in surface ectoderm cells with and without p63. Replicates were sequenced on Illumina NextSeq sequencer, and reads were aligned and filtered for valid long-range interactions using HiCPro. Results: Dynamic long-range interactions at the TFAP2C locus were detected with and without p63 in surface ectoderm cells. Conclusion: Long-range interactions detected via HiChIP were confirmed in the surface ectoderm by this technique, validating the HiChIP method through an orthogonal approach.

2018-11-06 | GSE114846 | GEO

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