{"lab": {"status": "current", "correspondence": [{"contact_email": "dmFoZWRpQHBlbm5tZWRpY2luZS51cGVubi5lZHU=", "@id": "/users/a44efbbf-7993-4258-b1ed-88045387e8ba/", "display_title": "Golnaz Vahedi"}], "@id": "/labs/golnaz-vahedi-lab/", "@type": ["Lab", "Item"], "title": "Golnaz Vahedi, UPENN", "display_title": "Golnaz Vahedi, UPENN", "uuid": "fedfc81d-f1ce-4203-9c87-bc0b6eb2bfc3", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.fedfc81d-f1ce-4203-9c87-bc0b6eb2bfc3"]}}, "award": {"@type": ["Award", "Item"], "center_title": "OFHHD - Phillips-Cremins", "project": "4DN", "description": "OFHHD: Short tandem repeat regions (STR) are distributed evenly across the human genome, and recent genome-wide studies have demonstrated that STRs are polymorphic across individuals and linked to gene expression levels. STR instability at key genomic loci has been causally linked to disease pathophysiology in a range of expansion disorders. We recently demonstrated that nearly all disease-associated STRs co-localize with boundaries demarcating topologically associated domains (TADs). Moreover, we have observed that pathologic STR instability and transcriptional silencing can destroy the associated boundary and shift genomic loci to the nuclear periphery. These results now open critical unanswered questions regarding whether and how STR expansion and pathologic alterations in gene expression are functionally linked to boundary integrity and radial positioning. Here, we focus on the prototypic repeat expansion disorder Friedreich\u2019s ataxia (FRDA) in which expansion of a GAA STR in the first intron of the FRATAXIN (FXN) gene results in cardiac and neuronal pathology. The cardiac pathology, specifically hypertrophy, fibrosis, and occasional dilation of the ventricle, is the etiology of significant FRDA mortality. GAA expansion is associated with the silencing of FXN transcription and a repositioning of the locus to the nuclear periphery. However, it remains unclear if the change in genome folding, radial positioning, or reduced expression drives STR expansion or vice versa. A major technical barrier contributing to this knowledge gap is that STR instability and genome folding are classically evaluated in bulk populations, however they exhibit tremendous variation across individual somatic cells of the same subtype and among cell types within a pathologically affected tissue. Here, we seek to decipher the causal link among STR instability, transcription, radial positioning, and genome folding. Our central hypothesis is that disruption of long-range loops is the initial event triggered by STR expansion leading to a cascade of heterochromatin spreading, silencing, and loss of radial positioning. We will test our hypothesis by generating genome-wide, single-cell maps of chromatin accessibility, expression, and the repressive H3K9me3 heterochromatin mark in GAA-expanded and control iPS cells and iPS-derived cardiomyocytes. We will integrate genomics data with single-cell sequential Oligopaints/OligoSTORM imaging of TADs and local chromatin structure, as well as single molecule RNA FISH for FXN expression. We will implement multiple genome engineering strategies, including dCas9-VP64 FXN activation and dCas9-CTCF loop re-engineering in FRDA GAA-iPS cells, and dCas9-Krab-Dnmt3a FXN silencing and dCas9-Krab CTCF-mediated loop disruption in healthy iPS cells. We will assay the effect of genome engineering approaches on TADs, radial positioning, STR length, and FXN expression in single cells. Successful completion of the proposed work will shed light on the pathophysiological mechanisms underlying repeat expansion disorders by deciphering the cause-and-effect relationships among genome folding, radial positioning, transcription, and STR expansion.", "display_title": "SINGLE-CELL DISSECTION OF CHROMATIN ARCHITECTURE MECHANISMS CONNECTING PATHOLOGIC INSTABILITY AND TRANSCRIPTIONAL SILENCING", "status": "current", "uuid": "8c9d595e-2809-4779-ae6e-305341f695ff", "@id": "/awards/1U01DA052715-01/", "name": "1U01DA052715-01", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "study": "TCF1 protein in thymocytes", "status": "released", "aliases": ["golnaz-vahedi-lab:expset_hi-c_scid.adh-T-cell-diff-KO-tcf1"], "accession": "4DNES1TMKQAN", "condition": "CRISPR modified- Knockout tcf7", "description": "in situ Hi-C on TCF1 KO Scid.adh cell line", "study_group": "Disrupted or Atypical Cells", "date_created": "2022-10-18T15:56:38.067695+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Hi-C on Scid.adh cells", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-07-18T06:46:02.067911+00:00"}, "public_release": "2022-12-12", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "c4f598be-227c-44be-a67e-62b1879478e8", "@id": "/experiments-hi-c/4DNEXK1LDDDU/", "accession": "4DNEXK1LDDDU", "display_title": "in situ Hi-C on scid.adh with Arima - A1, A2 - 4DNEXK1LDDDU", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "82ab57a8-e1f7-469c-afab-da5dc3a53555", "@id": "/experiments-hi-c/4DNEXUYDF7OO/", "accession": "4DNEXUYDF7OO", "display_title": "in situ Hi-C on scid.adh with Arima - A1, A2 - 4DNEXUYDF7OO", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"award": {"uuid": "8c9d595e-2809-4779-ae6e-305341f695ff", "@id": "/awards/1U01DA052715-01/", "status": "current", "@type": ["Award", "Item"], "display_title": "SINGLE-CELL DISSECTION OF CHROMATIN ARCHITECTURE MECHANISMS CONNECTING PATHOLOGIC INSTABILITY AND TRANSCRIPTIONAL SILENCING", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "115439ec-470f-4798-aec4-945f61cf5136", "title": "4DNES1TMKQAN - Processed files", "contributing_labs": [], "name": "115439ec-470f-4798-aec4-945f61cf5136", "@id": "/higlass-view-configs/115439ec-470f-4798-aec4-945f61cf5136/", "@type": ["HiglassViewConfig", "UserContent", "Item"], "status": "released", "display_title": "4DNES1TMKQAN - Processed files", "description": "4DNES1TMKQAN (in situ Hi-C on TCF1 KO Scid.adh cell line): 4DNFIKHGZ22V, 4DNFIHLYV5ZY, 4DNFI1N65MWL, 4DNFIFPJ7FZO", "filetype": "HiglassViewConfig", "lab": {"status": "current", "uuid": "fedfc81d-f1ce-4203-9c87-bc0b6eb2bfc3", "display_title": "Golnaz Vahedi, UPENN", "@type": ["Lab", "Item"], "@id": "/labs/golnaz-vahedi-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.fedfc81d-f1ce-4203-9c87-bc0b6eb2bfc3"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}, "location": "tab:processed-files", "description": "auto_generated_higlass_view_config"}], "static_headers": [{"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "<b>In Situ Hi-C</b>\n\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\">Rao et al., 2014</a> for more details.\n</p>\n\n<div>\n<img style=\"width: 600px;max-width:100%;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\"/>\n  <br/><br/>\n  <em>Image source: Rao et al., 2014, Figure 1A</em>\n</div>", "name": "item-page-headers.ExperimentType.insituhic", "award": {"status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Assay Description", "status": "released", "aliases": ["4dn-dcic-lab:experiment_infobox_hic"], "options": {"filetype": "html", "collapsible": false, "default_open": false, "convert_ext_links": true}, "date_created": "2018-09-07T18:19:43.777198+00:00", "section_type": "Item Page Header", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2023-11-09T14:48:01.220007+00:00"}, "schema_version": "2", "@id": "/static-sections/298554ad-20e2-4449-a752-ac190123dab7/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "298554ad-20e2-4449-a752-ac190123dab7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.56c9c683-bb11-471b-b590-c656f7dc03c1"]}, "display_title": "Assay Description", "external_references": [], "content": "<b>In Situ Hi-C</b>\n\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\">Rao et al., 2014</a> for more details.\n</p>\n\n<div>\n<img style=\"width: 600px;max-width:100%;\" src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\"/>\n  <br/><br/>\n  <em>Image source: Rao et al., 2014, Figure 1A</em>\n</div>", "filetype": "html", "content_as_html": "<div class=\"html-container\"><b>In Situ Hi-C</b>\n<p>\n   In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n</p>\n<p>\nSee <a href=\"https://www.sciencedirect.com/science/article/pii/S0092867414014974?via%3Dihub\" rel=\"noopener noreferrer\" target=\"_blank\">Rao et al., 2014</a> for more details.\n</p>\n<div>\n<img src=\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\" style=\"width: 600px;max-width:100%;\"/>\n<br/><br/>\n<em>Image source: Rao et al., 2014, Figure 1A</em>\n</div></div>"}], "processed_files": [{"accession": "4DNFI3W7M5AB", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCm38", "file_type_detailed": "contact list-combined (pairs)", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "display_title": "pairs", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFI3W7M5AB.pairs.gz", "md5sum": "c0eb9872da60a908a0f46479f7243ced", "file_type": "contact list-combined", "file_classification": "processed file", "file_size": 14914639451, "upload_key": "bf887819-ad63-4bf5-835f-9fb61232a42d/4DNFI3W7M5AB.pairs.gz", "@id": "/files-processed/4DNFI3W7M5AB/", "href": "/files-processed/4DNFI3W7M5AB/@@download/4DNFI3W7M5AB.pairs.gz", "uuid": "bf887819-ad63-4bf5-835f-9fb61232a42d", "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/bf887819-ad63-4bf5-835f-9fb61232a42d/4DNFI3W7M5AB.pairs.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "extra_files": [{"href": "/files-processed/4DNFI3W7M5AB/@@download/4DNFI3W7M5AB.pairs.gz.px2", "file_size": 9467285, "md5sum": "e4feab66b1564969aad934ca2d11346c", "file_format": {"@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "display_title": "pairs_px2", "file_format": "pairs_px2", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"Total reads": 1023322314, "status": "released", "display_title": "QualityMetricPairsqc from 2022-11-27", "uuid": "87f59adb-6e8a-4dd4-922a-aa51adabacc1", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "@id": "/quality-metrics-pairsqc/87f59adb-6e8a-4dd4-922a-aa51adabacc1/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3W7M5AB/pairsqc_report.html", "overall_quality_status": "PASS", "quality_metric_summary": [{"title": "Filtered Reads", "value": "1023322314", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "60.392", "tooltip": "Percent of filtered reads (=618.0m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "29.981", "tooltip": "Percent of filtered reads (=306.8m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "9.628", "tooltip": "Percent of filtered reads (=98.52m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "lab": {"status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"display_title": "Golnaz Vahedi, UPENN", "uuid": "fedfc81d-f1ce-4203-9c87-bc0b6eb2bfc3", "name": "golnaz-vahedi-lab", "@type": ["Lab", "Item"], "@id": "/labs/golnaz-vahedi-lab/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.fedfc81d-f1ce-4203-9c87-bc0b6eb2bfc3"]}}], "external_references": [], "track_and_facet_info": {"dataset": "Hi-C on Scid.adh cells", "condition": "CRISPR modified- Knockout tcf7", "experimental_lab": "Golnaz Vahedi, UPENN", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "Arima - 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A1, A2", "biosource_name": "scid.adh", "lab_name": "4DN DCIC, HMS"}, "last_modified": {"date_modified": "2023-06-21T18:24:04.031416+00:00"}}, {"accession": "4DNFIKHGZ22V", "higlass_uid": "57e127bd-4f47-46dd-9b5b-961b4e5158bd", "@type": ["FileProcessed", "File", "Item"], "genome_assembly": "GRCm38", "file_type_detailed": "contact matrix (mcool)", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/mcool/", "display_title": "mcool", "status": "released", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFIKHGZ22V.mcool", "notes_to_tsv": ["WARNING - Due to a bug in the version of cooler (0.8.3) used in the current 4DN standard Hi-C processing pipeline some pixels may occur mulitple times at a single resolution with different counts being reported for each occurence.  This duplication does not affect the higlass display of these files, howevver, downstream analyses using this file may encounter issues due to this pixel duplication.  The counts from the duplicate pixels can be aggregated to determine the correct count value at that location. If this issue is problematic for your needs you should consider regenerating the matrices from the merged pairs file of the associated dataset using a more recent version of cooler.  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