This paper studies how two experimental variables - \ncross-linking method and enzyme - affect in situ Hi-C and \nMicro-C assays.\nThe tables below present all the data from the paper, \nhighlighting the variables investigated.\nThe datasets are divided in three groups:
\nThe optimized in situ Hi-C 3.0 protocol can be found here.
All experimental conditions investigated are reported here for documentation purposes.\nUsers interested in using Hi-C or Micro-C data from this project for alternative analyses are advised to use only datasets generated with the optimal cross-linking conditions of 1% Formaldehyde + 3mM DSG.\nOther datasets may be obtained with non-optimal cross-linking conditions (as demonstrated in the paper).\nThe authors further advise users to carefully select digestion enzymes and library size to fit their needs.
A matrix of Experiment Sets investigating all combinations of experimental variables at lower sequencing depth.
\nA matrix of Experiment Sets investigating all combinations of experimental variables at lower sequencing depth.
\nA group of Experiment Sets with optimal cross-linking condition at higher sequencing depth.
\nA group of Experiment Sets with optimal cross-linking condition at higher sequencing depth.
\nAdditional Experiment Sets including ATAC-seq, CUT&RUN and CUT&Tag.
\nAdditional Experiment Sets including ATAC-seq, CUT&RUN and CUT&Tag.
\nAll experimental conditions investigated are reported here for documentation purposes.\nUsers interested in using Hi-C or Micro-C data from this project for alternative analyses are advised to use only datasets generated with the optimal cross-linking conditions of 1% Formaldehyde + 3mM DSG.\nOther datasets may be obtained with non-optimal cross-linking conditions (as demonstrated in the paper).\nThe authors further advise users to carefully select digestion enzymes and library size to fit their needs.
For deeply sequenced data, the study authors recommend the following datasets for\n in situ Hi-C 3.0 (with cross-linking 1% Formaldehyde and 3mM DSG, enzymes DpnII and DdeI)\n and Micro-C (with cross-linking 1% Formaldehyde and 3mM DSG):\n
\nFor deeply sequenced data, the study authors recommend the following datasets for\n in situ Hi-C 3.0 (with cross-linking 1% Formaldehyde and 3mM DSG, enzymes DpnII and DdeI)\n and Micro-C (with cross-linking 1% Formaldehyde and 3mM DSG):\n
\nFor other conditions with optimal cross-linking \n(1% Formaldehyde and 3mM DSG), the study authors advise the following datasets\n(note that most have lower sequencing depth):\n
\nFor other conditions with optimal cross-linking \n(1% Formaldehyde and 3mM DSG), the study authors advise the following datasets\n(note that most have lower sequencing depth):\n
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