EXPERIMENT_TITLE: Illumina HiSeq 2500 paired end sequencing
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Each Hi-C library was generated from 20 million cells to have enough material to perform the capture step, following the protocol described previously 32 with the following modifications. The ligation process was performed overnight at 16 °C instead of 4 hours and the samples were treated 1 hr at 37 °C with RNAse A (1 µg/ml, Thermo Fisher Scientific, #EN0531) before reversing the crosslink. Finally, the removal of the biotin from un-ligated ends were performed following the protocol described in 1. After removal of biotin-marked non-ligated DNA ends, 5-9 µg of biotinylated DNA was fragmented on a Covaris™ E220 in order to reach final fragment sizes of ~150-300 bp. The sheared DNA was end-repaired, adenylated, the biotinylated Hi-C products were pooled down with Dynabeads™ MyOne™ Streptavidin C1 solution (Thermo Fisher Scientific, #65001), ligated to IDT adaptors with unique dual-matched indexes (Integrated DNA Technologies) and amplified with 8 PCR cycles using the KAPA HiFi HotStart ReadyMix (2X) (Roche Kapa Biosystems).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The linear sequence of DNA provides invaluable information about the nature of genes, the regulatory elements and their distribution along chromosomes. However, to fully understand gene function and regulation we need to dissect how genes are physically folded in the 3-D nuclear space. Here we describe immuno-OligoSTORM (iOS), an imaging strategy to simultaneously image the DNA and histones in super-resolution to resolve the distribution of nucleosomes within specific genes at the nanoscale level. We combined iOS with an innovative coarse-grained modeling approach to integrate the super resolution imaging data with Hi-C contact frequencies and deconvoluted MNase-seq information. This novel method, called Modeling immuno-OligoSTORM (MiOS), allows quantitative modeling of genes at basepair resolution. With MiOS we explored intercellular variability and transcriptional dependent gene conformation of housekeeping and pluripotency-related genes in human pluripotent and differentiated cells with the highest degree of data integration achieved so far.
SAMPLE_TITLE: Capture HiC in human induced PSC-1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "ENA first public", "VALUE": "2021-06-29"}, {"TAG": "ENA-LAST-UPDATE", "VALUE": "2022-06-08"}, {"TAG": "External Id", "VALUE": "SAMEA7757610"}, {"TAG": "INSDC center alias", "VALUE": "Institute for research in Biomedecine"}, {"TAG": "INSDC center name", "VALUE": "Institute for research in Biomedecine"}, {"TAG": "INSDC first public", "VALUE": "2021-06-29T00:19:27Z"}, {"TAG": "INSDC last update", "VALUE": "2022-06-08T16:56:14Z"}, {"TAG": "INSDC status", "VALUE": "public"}, {"TAG": "Submitter Id", "VALUE": "hic_hipsc_rep1_lane1"}, {"TAG": "cell type", "VALUE": "iPSC"}, {"TAG": "common name", "VALUE": "human"}, {"TAG": "sample name", "VALUE": "hic_hipsc_rep1_lane1"}]
Pool_Member_@attributes_sample_title: Capture HiC in human induced PSC-1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Capture HiC in human induced PSC-1
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