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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Six in situ Hi-C libraries of control and mESC auxin-inducible degrons for Scc1 and Ring1b.

ABSTRACT: In this experiment, we've examined chromatin conformation differences of E14 mESC against cohesin and Ring1b degrons. We performed a modified in situ Hi-C protocol from (Rao et al., 2014) that can be found in detail at (Díaz et al., 2018). Samples were digested with MboI restriction enzyme. The aim of the experiment was to characterize the role of cohesin and polycomb on the 3D structure of mouse chromatin.

INSTRUMENT(S): NextSeq 550

ORGANISM(S): Mus musculus

SUBMITTER: Juan Vaquerizas

PROVIDER: E-MTAB-7816 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Chromatin contact maps of 24 and 48 hours post-fertilisation zebrafish (Danio rerio) embryos and 48 hours post-fertilisation fibroblasts

Project description:In this experiment, we've examined chromatin conformation of zebrafish embryos at 24 and 48 hours post-fertilization (hpf), as well as 48 hpf fibroblasts. The aim of this study was to characterise the 3D chromatin structure of zebrafish and perform an evolutionary comparison with mammalian genomes (Homo sapiens and Mus musculus) focusing on syntenic regions and zebrafish ohnologs (duplicated genes that were kept in the genome after the third round of whole-genome duplication).

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Project description:In this experiment, we've examined chromatin conformation of mESCs and 2C-like cells generated from a CAF-1 knockdown. The method to generate the knockdown was described in (). We performed a modified in situ Hi-C protocol from (Rao et al., 2014) and that can be found in detail at (Díaz et al., 2017, under revision). Samples were digested with MboI restriction enzyme having as starting material 100k cells with two biological replicates per sampling point. The aim of the experiment was to analyze the potential chromatin conformational changes that accompany the mESC to 2C-like transition.

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Low input Hi-C datasets for a diffuse large B-cell lymphoma sample, healthy control human B-cells and mouse embryonic stem cells

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Capture-C experiments on auxin treated control (E14-Tir) and Scc1-AID, Ring1b-AID, Ring1b-AID-Scc1-AID and CTCF-AID (with and without a 6-hour auxin treatment) cells

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