EXPERIMENT_TITLE: GSM7926239: in situ Hi-C on CyT49 differentiated to pancreatic endoderm with MboI - 4DNEXJH3AAC8; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: description: The Official 4DN Standard in situ Hi-C protocol adapted from Rao et al. 2014 PMID: 25497547 - with accepted deviations approved by SC 02/21/2017 download: https://data.4dnucleome.org/protocols/fdc20e37-f22e-42dc-8026-0a132739bad1/@@download/attachment/4DN_in_situ_Hi-C_protocol_20170729.pdf
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Replicates of Hi-C on CyT49 cells differentiated to pancreatic endoderm Overall design: **Data Use Guidelines:** This is a data set generated by the 4DN Network and made freely available to the scientific community. If you are intending to use these data for a publication, we ask that you please contact the data generating lab to discuss possible coordinated publication. In your manuscript, please cite the 4DN White Paper ([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884)) and the 4DN Data Portal paper ([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), and please acknowledge the 4DN lab which generated the data. Please direct any questions to the [Data Coordination and Integration Center](mailto:support@4dnucleome.org). lab: Bing Ren, UCSD award: 1U54DK107977-01 accession: 4DNESOLVRKBM condition: pancreatic endoderm submitted_by: Bin Li dataset_label: Hi-C on hESC differentiated to pancreatic endoderm experiment_type: in situ Hi-C url: https://data.4dnucleome.org/experiment-set-replicates/4DNESOLVRKBM/ number_of_experiments: 2 experiment: 4DNEXON87MIM; replicate_number: Biorep 1, Techrep 1 experiment: 4DNEXJH3AAC8; replicate_number: Biorep 2, Techrep 1 Series supplementary files: *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/f81352af-bd42-44c5-86b6-b04de82c4014/ genome_assembly: GRCh38 derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIELSHHII.pairs.gz, 4DNFITKCX2DO.pairs.gz, 4DNFI823L812.txt description: This is an output file of the Hi-C processing pipeline file_type: contact list-combined file_format: pairs file name: 4DNFISAJ77X3.pairs.gz *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/f81352af-bd42-44c5-86b6-b04de82c4014/ genome_assembly: GRCh38 derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIELSHHII.pairs.gz, 4DNFITKCX2DO.pairs.gz, 4DNFI823L812.txt description: This is an output file of the Hi-C processing pipeline file_type: contact matrix file_format: mcool file name: 4DNFIK3NF6R2.mcool *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/2e9ab254-25fa-4f6b-8eee-51cbce38bed4/ genome_assembly: GRCh38 derived_from: 4DNFIK3NF6R2.mcool description: Boundaries calls on Hi-C contact matrices file_type: boundaries file_format: bed file name: 4DNFI7SHVNYK.bed.gz *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/2e9ab254-25fa-4f6b-8eee-51cbce38bed4/ genome_assembly: GRCh38 derived_from: 4DNFIK3NF6R2.mcool description: Diamond insulation scores calls on Hi-C contact matrices file_type: insulation score-diamond file_format: bw file name: 4DNFI9EBDZ2I.bw *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/f2d06a88-2eee-4fe7-bf8f-ab9342d97557/ genome_assembly: GRCh38 derived_from: 4DNFIK3NF6R2.mcool, 4DNFI7MCA4R6.bedGraph.gz description: Compartments signals on Hi-C contact matrices file_type: compartments file_format: bw file name: 4DNFI32O4LL2.bw
SAMPLE_TITLE: in situ Hi-C on CyT49 differentiated to pancreatic endoderm with MboI - 4DNEXJH3AAC8
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "biosource_summary: CyT49 differentiated to pancreatic endoderm"}, {"TAG": "cell_line", "VALUE": "CyT49"}, {"TAG": "tissue", "VALUE": "pancreatic endoderm"}, {"TAG": "modifications_summary", "VALUE": "None"}, {"TAG": "Sex", "VALUE": "male"}, {"TAG": "treatments_summary", "VALUE": "None"}, {"TAG": "biosample_type", "VALUE": "in vitro differentiated cells"}, {"TAG": "url", "VALUE": "https://data.4dnucleome.org/biosamples/4DNBSCF458L5/"}, {"TAG": "life_stage", "VALUE": "embryonic"}]
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