{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8535CXVX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8535CXVX",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane2_exprs"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003660/",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8535CXVX](/measurement-sets/IGVFDS8535CXVX/) has sequence file(s): [IGVFFI4178JMGA](/sequence-files/IGVFFI4178JMGA/), [IGVFFI6555USZE](/sequence-files/IGVFFI6555USZE/), [IGVFFI1996TPSI](/sequence-files/IGVFFI1996TPSI/), [IGVFFI9942XRES](/sequence-files/IGVFFI9942XRES/), [IGVFFI0180MAUH](/sequence-files/IGVFFI0180MAUH/), [IGVFFI8003IBBB](/sequence-files/IGVFFI8003IBBB/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS8535CXVX/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8929VNCP](/auxiliary-sets/IGVFDS8929VNCP/) has sequence file(s): [IGVFFI6893EPCL](/sequence-files/IGVFFI6893EPCL/), [IGVFFI0355AKWQ](/sequence-files/IGVFFI0355AKWQ/), [IGVFFI7148JTBN](/sequence-files/IGVFFI7148JTBN/), [IGVFFI5295OHTL](/sequence-files/IGVFFI5295OHTL/), [IGVFFI3658HZBE](/sequence-files/IGVFFI3658HZBE/), [IGVFFI0332PBFZ](/sequence-files/IGVFFI0332PBFZ/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS8929VNCP/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8929VNCP/",
"accession": "IGVFDS8929VNCP",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane2_CS1"
],
"file_set_type": "gRNA sequencing"
}
],
"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"
},
"control_for": [],
"creation_timestamp": "2023-12-08T23:53:37.798405+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"accession": "IGVFDO9208RPQQ",
"aliases": [
"igvf:donor_of_K562"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4178JMGA/",
"accession": "IGVFFI4178JMGA",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_exprs_10Xlane2_seqlane1_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:19.295766+00:00",
"file_format": "fastq",
"file_size": 2303957168,
"href": "/sequence-files/IGVFFI4178JMGA/@@download/IGVFFI4178JMGA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/8793cf75-3378-4865-80d0-ce35997f1724/IGVFFI4178JMGA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"term_name": "Illumina NextSeq 2000"
},
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/K562_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAHG2HHV/VP64_exprs_2/VP64_exprs_2_S2_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6555USZE/",
"accession": "IGVFFI6555USZE",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_exprs_10Xlane2_seqlane1_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:20.387394+00:00",
"file_format": "fastq",
"file_size": 4944095273,
"href": "/sequence-files/IGVFFI6555USZE/@@download/IGVFFI6555USZE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/7548302f-b2ba-4829-8437-dd94797341c8/IGVFFI6555USZE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"term_name": "Illumina NextSeq 2000"
},
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/K562_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAHG2HHV/VP64_exprs_2/VP64_exprs_2_S2_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1996TPSI/",
"accession": "IGVFFI1996TPSI",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_exprs_10Xlane2_seqlane1_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:18.238575+00:00",
"file_format": "fastq",
"file_size": 735237103,
"href": "/sequence-files/IGVFFI1996TPSI/@@download/IGVFFI1996TPSI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/8708a697-1f4b-4e10-8290-823504d027ac/IGVFFI1996TPSI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"term_name": "Illumina NextSeq 2000"
},
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/K562_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAHG2HHV/VP64_exprs_2/VP64_exprs_2_S2_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9942XRES/",
"accession": "IGVFFI9942XRES",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_exprs_10Xlane2_seqlane2_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:22.280229+00:00",
"file_format": "fastq",
"file_size": 739506137,
"href": "/sequence-files/IGVFFI9942XRES/@@download/IGVFFI9942XRES.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/13d77472-ae7a-4fc9-82c3-22fbd56403fe/IGVFFI9942XRES.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"term_name": "Illumina NextSeq 2000"
},
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/K562_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAHG2HHV/VP64_exprs_2/VP64_exprs_2_S2_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0180MAUH/",
"accession": "IGVFFI0180MAUH",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_exprs_10Xlane2_seqlane2_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:23.427647+00:00",
"file_format": "fastq",
"file_size": 2326924306,
"href": "/sequence-files/IGVFFI0180MAUH/@@download/IGVFFI0180MAUH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/6cbf1d6d-e99f-4e38-80f3-5f365bfd2209/IGVFFI0180MAUH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"term_name": "Illumina NextSeq 2000"
},
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/K562_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAHG2HHV/VP64_exprs_2/VP64_exprs_2_S2_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8003IBBB/",
"accession": "IGVFFI8003IBBB",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_exprs_10Xlane2_seqlane2_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:24.554194+00:00",
"file_format": "fastq",
"file_size": 4957888982,
"href": "/sequence-files/IGVFFI8003IBBB/@@download/IGVFFI8003IBBB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/d8a6ba2b-fa8e-4050-9f76-05b336d998df/IGVFFI8003IBBB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"term_name": "Illumina NextSeq 2000"
},
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/K562_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAHG2HHV/VP64_exprs_2/VP64_exprs_2_S2_L002_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_file_set_for": [
"/analysis-sets/IGVFDS9078ZWQH/"
],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"notes": "The readout 86015c12-b9a6-43ba-9601-5d75aab4d39c was removed from this measurement set. This measurement set previously did not specify a preferred_assay_title, but the property is now required so it has been defaulted to SUPERSTARR. Please update with an appropriate preferred_assay_title.",
"preferred_assay_title": "scCRISPR screen",
"protocols": [
"https://www.protocols.io/view/methods-from-multiplex-single-cell-crispra-screeni-c5zvy766"
],
"publications": [
{
"@id": "/publications/20fcbdbb-5a47-41c6-b80b-e6dd0e8a8d3e/",
"publication_identifiers": [
"doi:10.1101/2023.03.28.534017"
]
}
],
"release_timestamp": "2024-08-13T20:47:08.854198+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9390JSDH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9390JSDH",
"aliases": [
"jay-shendure:CRISPRa_VP64_K562_10Xlane2"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS7581DNXF/",
"accession": "IGVFDS7581DNXF",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci"
}
],
"modifications": [
{
"@id": "/crispr-modifications/ee99bf66-2a5a-4ec6-8380-9434b259afd1/",
"modality": "activation"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:K562"
],
"status": "released",
"summary": "K562",
"term_name": "K562"
}
],
"status": "released",
"summary": "K562 cell line (cellular sub pool: 10Xlane2), female, Homo sapiens modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "21",
"status": "released",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"submitted_files_timestamp": "2023-12-09T00:50:01.911165+00:00",
"summary": "scCRISPR activation screen integrating a guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci",
"uuid": "f334df0a-43a4-4dc1-aac9-d76cc4af7087"
}