EXPERIMENT_TITLE: GSM7926240: in situ Hi-C on CyT49 with MboI - 4DNEX94DX4XP; 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 undifferentiated CyT49 human embryonic stem cells 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: 4DNESSSDVO27 condition: undifferentiated 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/4DNESSSDVO27/ number_of_experiments: 2 experiment: 4DNEX94DX4XP; replicate_number: Biorep 1, Techrep 1 experiment: 4DNEXFRAFIWZ; replicate_number: Biorep 2, Techrep 1 Series supplementary files: *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/ffd4e6a8-1ad3-40d9-97fa-ad1bbfbdb94d/ genome_assembly: GRCh38 derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI9VR75SS.pairs.gz, 4DNFIKGQSUNZ.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: 4DNFI3WK3QYQ.pairs.gz *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/ffd4e6a8-1ad3-40d9-97fa-ad1bbfbdb94d/ genome_assembly: GRCh38 derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI9VR75SS.pairs.gz, 4DNFIKGQSUNZ.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: 4DNFIXOWKAM6.mcool *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/97a9ea35-ef5c-4c52-9ac0-11391794a02d/ genome_assembly: GRCh38 derived_from: 4DNFIXOWKAM6.mcool description: Boundaries calls on Hi-C contact matrices file_type: boundaries file_format: bed file name: 4DNFI23RGV8B.bed.gz *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/97a9ea35-ef5c-4c52-9ac0-11391794a02d/ genome_assembly: GRCh38 derived_from: 4DNFIXOWKAM6.mcool description: Diamond insulation scores calls on Hi-C contact matrices file_type: insulation score-diamond file_format: bw file name: 4DNFIKIGIIY4.bw *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/a5ed29eb-493f-46ab-a599-416b15bc3a1f/ genome_assembly: GRCh38 derived_from: 4DNFIXOWKAM6.mcool, 4DNFI7MCA4R6.bedGraph.gz description: Compartments signals on Hi-C contact matrices file_type: compartments file_format: bw file name: 4DNFIN3O5SOJ.bw
SAMPLE_TITLE: in situ Hi-C on CyT49 with MboI - 4DNEX94DX4XP
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