{
"@context": "/terms/",
"@id": "/construct-library-sets/IGVFDS7581DNXF/",
"@type": [
"ConstructLibrarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS7581DNXF",
"aliases": [
"jay-shendure:construct_library_CRISPRa_Chardon-McDiarmid"
],
"applied_to_samples": [
{
"@id": "/in-vitro-systems/IGVFSM8382KOXO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8382KOXO",
"aliases": [
"jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane4"
],
"classifications": [
"differentiated cell specimen"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sp-dCas9-VPH"
}
],
"nucleic_acid_delivery": "nucleofection",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to neuron for 19 days (cellular sub pool: 10Xlane4) modified with CRISPRa Sp-dCas9-VPH, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000540/",
"status": "released",
"term_name": "neuron"
}
},
{
"@id": "/in-vitro-systems/IGVFSM1594ZOQH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1594ZOQH",
"aliases": [
"jay-shendure:CRISPRa_VPR_K562_10Xlane1"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/8b61bce4-105c-435e-9b32-1c8903566a9b/",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sp-dCas9-VP64-p65-Rta (VPR)"
}
],
"nucleic_acid_delivery": "nucleofection",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"status": "released",
"term_name": "K562"
}
],
"status": "released",
"summary": "Homo sapiens (female) K562 cell line (cellular sub pool: 10Xlane1) modified with CRISPRa Sp-dCas9-VP64-p65-Rta (VPR), transfected with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM9003EMOQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9003EMOQ",
"aliases": [
"jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons"
],
"classifications": [
"differentiated cell specimen"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sp-dCas9-VPH"
}
],
"nucleic_acid_delivery": "nucleofection",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to neuron for 19 days modified with CRISPRa Sp-dCas9-VPH, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000540/",
"status": "released",
"term_name": "neuron"
}
},
{
"@id": "/in-vitro-systems/IGVFSM8338YZLA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8338YZLA",
"aliases": [
"jay-shendure:CRISPRa_VPR_K562"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/8b61bce4-105c-435e-9b32-1c8903566a9b/",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sp-dCas9-VP64-p65-Rta (VPR)"
}
],
"nucleic_acid_delivery": "nucleofection",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"status": "released",
"term_name": "K562"
}
],
"status": "released",
"summary": "Homo sapiens (female) K562 cell line modified with CRISPRa Sp-dCas9-VP64-p65-Rta (VPR), transfected with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM9913PXTT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9913PXTT",
"aliases": [
"jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane2"
],
"classifications": [
"differentiated cell specimen"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sp-dCas9-VPH"
}
],
"nucleic_acid_delivery": "nucleofection",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to neuron for 19 days (cellular sub pool: 10Xlane2) modified with CRISPRa Sp-dCas9-VPH, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000540/",
"status": "released",
"term_name": "neuron"
}
},
{
"@id": "/in-vitro-systems/IGVFSM8317ZTFV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8317ZTFV",
"aliases": [
"jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane3"
],
"classifications": [
"differentiated cell specimen"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sp-dCas9-VPH"
}
],
"nucleic_acid_delivery": "nucleofection",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to neuron for 19 days (cellular sub pool: 10Xlane3) modified with CRISPRa Sp-dCas9-VPH, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000540/",
"status": "released",
"term_name": "neuron"
}
},
{
"@id": "/in-vitro-systems/IGVFSM9778VZHD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9778VZHD",
"aliases": [
"jay-shendure:CRISPRa_VP64_K562"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/ee99bf66-2a5a-4ec6-8380-9434b259afd1/",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sp-dCas9-VP64"
}
],
"nucleic_acid_delivery": "nucleofection",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"status": "released",
"term_name": "K562"
}
],
"status": "released",
"summary": "Homo sapiens (female) K562 cell line modified with CRISPRa Sp-dCas9-VP64, transfected with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM9390JSDH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9390JSDH",
"aliases": [
"jay-shendure:CRISPRa_VP64_K562_10Xlane2"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/ee99bf66-2a5a-4ec6-8380-9434b259afd1/",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sp-dCas9-VP64"
}
],
"nucleic_acid_delivery": "nucleofection",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"status": "released",
"term_name": "K562"
}
],
"status": "released",
"summary": "Homo sapiens (female) K562 cell line (cellular sub pool: 10Xlane2) modified with CRISPRa Sp-dCas9-VP64, transfected with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM9542NUGS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9542NUGS",
"aliases": [
"jay-shendure:CRISPRa_VPR_K562_10Xlane2"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/8b61bce4-105c-435e-9b32-1c8903566a9b/",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sp-dCas9-VP64-p65-Rta (VPR)"
}
],
"nucleic_acid_delivery": "nucleofection",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"status": "released",
"term_name": "K562"
}
],
"status": "released",
"summary": "Homo sapiens (female) K562 cell line (cellular sub pool: 10Xlane2) modified with CRISPRa Sp-dCas9-VP64-p65-Rta (VPR), transfected with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM4521QSSO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4521QSSO",
"aliases": [
"jay-shendure:CRISPRa_VP64_K562_10Xlane1"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/ee99bf66-2a5a-4ec6-8380-9434b259afd1/",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sp-dCas9-VP64"
}
],
"nucleic_acid_delivery": "nucleofection",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"status": "released",
"term_name": "K562"
}
],
"status": "released",
"summary": "Homo sapiens (female) K562 cell line (cellular sub pool: 10Xlane1) modified with CRISPRa Sp-dCas9-VP64, transfected with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM7750SNNY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7750SNNY",
"aliases": [
"jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane1"
],
"classifications": [
"differentiated cell specimen"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sp-dCas9-VPH"
}
],
"nucleic_acid_delivery": "nucleofection",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to neuron for 19 days (cellular sub pool: 10Xlane1) modified with CRISPRa Sp-dCas9-VPH, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000540/",
"status": "released",
"term_name": "neuron"
}
}
],
"assay_titles": [
"scCRISPR screen"
],
"audit": {
"ERROR": [
{
"category": "upload status not validated",
"detail": "Tabular file [IGVFFI1174ARXR](/tabular-files/IGVFFI1174ARXR/) has `upload_status` invalidated. Validation error detail: {\"tabular_file_error\": {\"schema\": \"src/schemas/table_schemas/guide_rna_sequences.json\", \"error_number_limit\": 1000, \"number_of_errors\": 1000, \"missing-label\": {\"count\": 1, \"description\": \"Based on the schema there should be a label that is missing in the data's header.\", \"details\": [{\"row_number\": null, \"field_number\": 17, \"note\": \"\"}]}, \"incorrect-label\": {\"count\": 6, \"description\": \"One of the data source header does not match the field name defined in the schema.\", \"details\": [{\"row_number\": null, \"field_number\": 11, \"note\": \"\"}, {\"row_number\": null, \"field_number\": 12, \"note\": \"\"}]}, \"type-error\": {\"count\": 689, \"description\": \"The value does not match the schema type and format for this field.\", \"details\": [{\"row_number\": 2, \"field_number\": 14, \"note\": \"type is \\\"integer/default\\\"\"}, {\"row_number\": 2, \"field_number\": 15, \"note\": \"type is \\\"array/default\\\"\"}]}, \"missing-cell\": {\"count\": 304, \"description\": \"This row has less values compared to the header row (the first row in the data source). A key concept is that all the rows in tabular data must have the same number of columns.\", \"details\": [{\"row_number\": 2, \"field_number\": 17, \"note\": \"\"}, {\"row_number\": 3, \"field_number\": 17, \"note\": \"\"}]}, \"error_types\": [\"missing-label\", \"missing-cell\", \"incorrect-label\", \"type-error\"]}}. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/tabular-files/IGVFFI1174ARXR/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released construct library set [IGVFDS7581DNXF](/construct-library-sets/IGVFDS7581DNXF/) has revoked subobject tabular file [IGVFFI2463QNJD](/tabular-files/IGVFFI2463QNJD/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/construct-library-sets/IGVFDS7581DNXF/"
},
{
"category": "mismatched status",
"detail": "Released construct library set [IGVFDS7581DNXF](/construct-library-sets/IGVFDS7581DNXF/) has in progress subobject tabular file [IGVFFI1174ARXR](/tabular-files/IGVFFI1174ARXR/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/construct-library-sets/IGVFDS7581DNXF/"
}
]
},
"award": {
"@id": "/awards/HG011966/",
"component": "functional characterization"
},
"control_for": [],
"creation_timestamp": "2024-01-31T00:00:44.930724+00:00",
"documents": [
"/documents/78f1cb67-1051-407c-9953-ba2c39ada2ae/",
"/documents/3d73a398-8fbb-4158-933e-d977b5768c0d/"
],
"file_set_type": "guide library",
"file_sets": [
"/measurement-sets/IGVFDS2133JAFB/",
"/analysis-sets/IGVFDS4021XJLW/",
"/analysis-sets/IGVFDS9078ZWQH/",
"/auxiliary-sets/IGVFDS2532AVSC/",
"/auxiliary-sets/IGVFDS4621HUKP/",
"/measurement-sets/IGVFDS2385QENN/",
"/measurement-sets/IGVFDS4863BMGZ/",
"/auxiliary-sets/IGVFDS4502LQQH/",
"/auxiliary-sets/IGVFDS2220HHTN/",
"/measurement-sets/IGVFDS7395DPAD/",
"/auxiliary-sets/IGVFDS7598WPXV/",
"/auxiliary-sets/IGVFDS4834SKZS/",
"/auxiliary-sets/IGVFDS8386FNRJ/",
"/measurement-sets/IGVFDS0272VVTX/",
"/auxiliary-sets/IGVFDS8929VNCP/",
"/measurement-sets/IGVFDS9384BVGM/",
"/measurement-sets/IGVFDS8535CXVX/",
"/measurement-sets/IGVFDS0508ERUQ/"
],
"files": [],
"guide_type": "sgRNA",
"input_for": [],
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI1174ARXR/",
"accession": "IGVFFI1174ARXR",
"aliases": [
"jay-shendure:tabularfile_CRISPRa_guidefile_updated_Chardon-McDiarmid_updated"
],
"content_type": "guide RNA sequences",
"file_format": "tsv",
"status": "in progress",
"upload_status": "invalidated"
}
],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"large_scale_loci_list": {
"@id": "/tabular-files/IGVFFI2463QNJD/",
"accession": "IGVFFI2463QNJD",
"aliases": [
"jay-shendure:tabularfile_CRISPRa_guidefile_updated_Chardon-McDiarmid"
],
"status": "revoked"
},
"publications": [
{
"@id": "/publications/20fcbdbb-5a47-41c6-b80b-e6dd0e8a8d3e/",
"publication_identifiers": [
"doi:10.1038/s41467-024-52490-4"
],
"status": "released"
}
],
"release_timestamp": "2024-08-13T20:47:07.265644+00:00",
"schema_version": "11",
"scope": "loci",
"selection_criteria": [
"TF binding sites",
"candidate cis-regulatory elements"
],
"status": "released",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"summary": "guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci",
"uuid": "1043a27b-01ca-4314-8312-be6ab2fa35c4"
}