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LINE1 elements at Distal Junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells [UMI-4C]

ABSTRACT: In this study, we constructed UMI-4C profiles of 5 different genomic loci (viewpoints) in two H9 human hES cell lines - naïve and primed - in order to study the 3D chromatin contact maps of these selected loci.

ORGANISM(S): Homo sapiens

PROVIDER: GSE268665 | GEO | 2025/02/12

REPOSITORIES: GEO

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LINE1 elements at Distal Junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells [ATAC-seq]

Project description:In this study, we investigated the status of chromatin accessibility in naïve hES cells with DJ-LINE1 repression compared to control by Assay of Transposase Accessible Chromatin (ATAC)-seq.

2025-02-12 | GSE268677 | GEO

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

LINE1 elements at Distal Junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells [UMI-4C]

Project description:LINE1 elements at Distal Junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells [UMI-4C]

| PRJNA1118225 | ENA

LINE1 elements at Distal Junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells [RNA-seq]

Project description:In this study, we investigated whether RNA Pol II-mediated gene expression is affected by repression of DJ-LINE1. Guide RNAs targeting DJ-LINE1 or control genomic regions were transfected for 48h in CRISPRi naïve hESC.

2025-02-12 | GSE268669 | GEO

LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [ChIRP-seq,RSeT+DT H9]

Project description:In this study, we profiled for LINE1 binding loci in RSeT+DT naïve hES cells with the Chromatin Isolation by RNA Purification (ChIRP)-seq strategy. We followed a previously published ChIRP protocol described (Percharde et al. 2018; Lu et al. 2020).

2024-09-09 | GSE263289 | GEO

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.

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LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [RNA-Seq_Primed_H9_L1KD]

Project description:To study L1 knockdown effect in mTeSR primed hES cells

2024-09-07 | GSE232930 | GEO

LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [RNA-Seq_RSeT_H9_L1KD]

Project description:To study L1 knockdown effect in RSeT naïve hES cells

2024-09-07 | GSE232937 | GEO

LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [NAD-seq]

Project description:To investigate NADs associated DNAs in the naïve and primed hES cells.

2024-09-09 | GSE236234 | GEO

LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [scRNA-seq]

Project description:In this study, we investigated LINE1 (L1), a major family of transposon elements (TEs) in the human genome, in naive hES cells for its roles in regulating 8-cell (8C) stage-specific totipotent genes. We performed single-cell RNA-seq (scRNA-seq) to assess if L1 knockdown in RSeT+DT naive hES cells induces 8-cell-like cells (8CLCs), and profile the transcriptome changes in the cells.

2024-09-07 | GSE232938 | GEO

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