EXPERIMENT_TITLE: GSM3937414: eHi-C hiPSC-ATCC ACS-1011; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: For Hi-C, nuclei were extraced after fixing using a cell lysis buffer. For ChIP-seq, nuclei were extracted and chromatins were fragmented by sonication. The TF/histone-DNA complexes were isolated by antibody.     Total RNA was isolated from samples by RNeasy Mini Kit (Qiagen) according to the manufacturer?s instructions. For eHi-C, briefly, the cells and tissues were first fixed with 1% formaldehyde and then quenched with 150mM glycine. The fixed samples were lysed using a cell lysis buffer or a tissue specific buffer. And nuclei were isolated and then digested with HindIII. After that, in situ proximity ligation was done by  ligating the digested chromatin in a large volume. Ligation products were then reverse-linked with proteinase K and purified using phenol-chloroform. The purified DNA was then digested with DpnII and then self ligated using T4 DNA ligase. After purification, the DNA products were then re-linearized with HindIII followed by DNA purification. The resulting DNA were used for library construction. First, the DNA were end-repaired using End-it kit (Epicentre). Second, the end repaired DNA was A-tailed by Klenow fragment (3??5? exo?; NEB). Then, a customized Illumina truseq Adapter was ligated and the resulting DNA was then PCR amplified. The final libraries were quantified and sequenced on Illumina Hiseq platform. All Hi-C libraries were constructed following illumina insctructions accompanying Truseq sample preparation kit.  Random indexes were introduced for eHi-C libraries to remove PCR duplication. Generally, PCR amplification was done with 7-9 cycles. All ChIP-seq libraries were generated following a ChIPmentation protocol with Nextera adapters.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Despite recent progress in mammalian 3D genome studies, it remains experimentally and computationally challenging to identify chromatin interactions genome-wide. Here we developed a highly efficient “easy Hi-C” (eHi-C) protocol that generates high-yield libraries with 0.1 million cells. After rigorous bias-correction with a significantly improved Hi-C analysis pipeline, we can directly recognize the dynamic long- and short-range chromatin loops from contact heatmaps. We compared 10 ultra-deep Hi-C or eHi-C datasets (billion- read scale) from human tissue- or cell types focusing on brain and neurogenesis. We found that H3K9me3 marks a 3D genome compartmental barrier for induced pluripotency. Dynamic chromatin loops, but not genome compartments, are hallmarks of neuronal differentiation and neuron-related diseases. Interestingly, we observed many neuron-specific enhancer-promoter looping clusters spanning Mb-scale neighborhoods, supporting a phase-separation model leading to enhancer aggregation during brain development. Taken together, our 3D genome analyses shed light on the regulation of brain development and complex neuronal diseases. Overall design: 3D genome structure mapping in human neurogenesis (from human induced pluripiotent stem cells to neural progenitor cells to neuron cells) using a newly designed easy Hi-C method ---------------------------------- GSM1267196: anchor_2_anchor.loop.H1.txt.gz GSM1267197: anchor_2_anchor.loop.H1.txt.gz GSM1055800: anchor_2_anchor.loop.IMR90.txt.gz GSM1055801: anchor_2_anchor.loop.IMR90.txt.gz GSM1154021: anchor_2_anchor.loop.IMR90.txt.gz GSM1154022: anchor_2_anchor.loop.IMR90.txt.gz GSM1154023: anchor_2_anchor.loop.IMR90.txt.gz GSM1154024: anchor_2_anchor.loop.IMR90.txt.gz GSM1055802: anchor_2_anchor.loop.IMR90.txt.gz GSM1055803: anchor_2_anchor.loop.IMR90.txt.gz GSM1154025: anchor_2_anchor.loop.IMR90.txt.gz GSM1154026: anchor_2_anchor.loop.IMR90.txt.gz GSM1154027: anchor_2_anchor.loop.IMR90.txt.gz GSM1154028: anchor_2_anchor.loop.IMR90.txt.gz GSM1181867: anchor_2_anchor.loop.GM12878.txt.gz GSM1181868: anchor_2_anchor.loop.GM12878.txt.gz GSM1551583: anchor_2_anchor.loop.GM12878.txt.gz GSM1551584: anchor_2_anchor.loop.GM12878.txt.gz GSM1551586: anchor_2_anchor.loop.GM12878.txt.gz GSM1608505: anchor_2_anchor.loop.GM12878.txt.gz GSM2054564: anchor_2_anchor.loop.CP.txt.gz GSM2054565: anchor_2_anchor.loop.CP.txt.gz GSM2054566: anchor_2_anchor.loop.CP.txt.gz GSM2054567: anchor_2_anchor.loop.GZ.txt.gz GSM2054568: anchor_2_anchor.loop.GZ.txt.gz GSM2054569: anchor_2_anchor.loop.GZ.txt.gz
SAMPLE_TITLE: eHi-C hiPSC-ATCC ACS-1011
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Foreskin Fibroblast Retroviral Reprogrammed, ATCC\u00ae ACS-1011"}, {"TAG": "cell type", "VALUE": "foreskin fibroblasts"}, {"TAG": "restrictive enzyme", "VALUE": "HindIII"}]
Pool_Member_@attributes_sample_title: eHi-C hiPSC-ATCC ACS-1011
RUN_SET_RUN_Pool_Member_@attributes_sample_title: eHi-C hiPSC-ATCC ACS-1011
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hiPSC_ACS-1011_eHiC_R1.fastq", "size": "163960173980", "date": "2021-02-25 09:43:09", "md5": "be31141b719da1bcbe2c19d855150ad7", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hiPSC_ACS-1011_eHiC_R2.fastq", "size": "163960173980", "date": "2021-02-25 07:50:58", "md5": "cca9fd3c7334946905d2533bb7e67033", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9676391", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9676391/SRR9676391", "size": "72765122211", "date": "2021-02-25 11:03:48", "md5": "bd153e83fc9a38705ca367315cef6920", "version": "2", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9676391.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR009/9676/SRR9676391/SRR9676391.lite.1", "size": "45163602895", "date": "2022-08-05 12:35:10", "md5": "bf2be12fc02b602f5d93414c0a75e834", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]