{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1140VRYN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1140VRYN",
"aliases": [
"jay-shendure:CRISPRa_singlevalidations_K562_ANXA1_rep2"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003090/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "bulk RNA-seq assay"
},
"audit": {},
"award": {
"@id": "/awards/HG011966/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/eb543cda-67b7-493c-84eb-187d0dac13ba/",
"title": "Jay Shendure"
},
"title": "Massively parallel characterization of variants and elements impacting transcriptional regulation in dynamic cellular systems"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS9531XJKW/",
"accession": "IGVFDS9531XJKW",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI9694NCRL/",
"accession": "IGVFFI9694NCRL",
"content_type": "guide RNA sequences",
"status": "in progress",
"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci"
}
],
"control_for": [],
"controlled_access": false,
"creation_timestamp": "2024-10-17T21:57:55.489297+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"accession": "IGVFDO9208RPQQ",
"aliases": [
"igvf:donor_of_K562"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI9832HTMK/",
"accession": "IGVFFI9832HTMK",
"aliases": [
"jay-shendure:CRISPRa_singlevalidations_K562_ANXA1_rep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-10-18T16:36:10.137663+00:00",
"file_format": "fastq",
"file_size": 103285797,
"href": "/sequence-files/IGVFFI9832HTMK/@@download/IGVFFI9832HTMK.fastq.gz",
"md5sum": "0a5d16cae35d582423d8034fea528d25",
"s3_uri": "s3://igvf-files/2024/10/18/7ed519b8-c3e9-4184-aad2-084ca7a27678/IGVFFI9832HTMK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "released",
"submitted_file_name": "/net/shendure/vol10/projects/IGVFtemp/pooled_fastqs/K562_gRNA_14_Rep_2_ANXA1_S2_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3522GLLP/",
"accession": "IGVFFI3522GLLP",
"aliases": [
"jay-shendure:seqspec_of_set_CRISPRa_singlevalidations_K562_ANXA1_rep2"
],
"content_type": "seqspec",
"creation_timestamp": "2025-04-08T21:11:44.420118+00:00",
"file_format": "yaml",
"file_size": 1018,
"href": "/configuration-files/IGVFFI3522GLLP/@@download/IGVFFI3522GLLP.yaml.gz",
"md5sum": "a72a97a7f0c97ba976ba9084e893135e",
"s3_uri": "s3://igvf-files/2025/04/08/c3609bc7-1e44-4c76-9661-878dbab1b6a2/IGVFFI3522GLLP.yaml.gz",
"status": "released",
"submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/seqspecs/CRISPRa-singleton-validations/CRISPRa_singleton_IGVFDS1140VRYN_seqspec_v3.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS3251QBOZ/"
],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"preferred_assay_title": "RNA-seq",
"protocols": [
"https://www.protocols.io/edit/methods-from-multiplex-single-cell-crispra-screeni-dscj6aun"
],
"publications": [
{
"@id": "/publications/20fcbdbb-5a47-41c6-b80b-e6dd0e8a8d3e/",
"publication_identifiers": [
"doi:10.1038/s41467-024-52490-4"
],
"status": "released"
}
],
"release_timestamp": "2025-05-29T21:02:02.218420+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4685GWVU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4685GWVU",
"aliases": [
"jay-shendure:CRISPRa_singletonvalidations_K562_rep2"
],
"classifications": [
"cell line"
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/40798097-3324-47f9-aa9b-3598e01224e4/",
"certificate_identifier": "IP118-02",
"controlled_access": false,
"status": "released"
}
],
"modifications": [
{
"@id": "/crispr-modifications/ee99bf66-2a5a-4ec6-8380-9434b259afd1/",
"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:K562"
],
"status": "released",
"summary": "K562",
"term_name": "K562"
}
],
"status": "released",
"summary": "Homo sapiens (female) K562 cell line modified with CRISPRa Sp-dCas9-VP64, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "29",
"status": "released",
"strand_specificity": "5 prime to 3 prime",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"submitted_files_timestamp": "2024-10-18T16:36:10.137663+00:00",
"summary": "CRISPR activation RNA-seq integrating a guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci",
"uuid": "4a2d5783-3b1f-48e9-93e8-5bffd4ff0fcf"
}