{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0508ERUQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0508ERUQ",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_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": "Auxiliary set [IGVFDS4834SKZS](/auxiliary-sets/IGVFDS4834SKZS/) has sequence file(s): [IGVFFI6797WWMA](/sequence-files/IGVFFI6797WWMA/), [IGVFFI4295KZWO](/sequence-files/IGVFFI4295KZWO/), [IGVFFI3777QEJF](/sequence-files/IGVFFI3777QEJF/), [IGVFFI1773NVFV](/sequence-files/IGVFFI1773NVFV/), [IGVFFI2340WJKO](/sequence-files/IGVFFI2340WJKO/), [IGVFFI2735DIDC](/sequence-files/IGVFFI2735DIDC/) 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/IGVFDS4834SKZS/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0508ERUQ](/measurement-sets/IGVFDS0508ERUQ/) has sequence file(s): [IGVFFI5956RRFZ](/sequence-files/IGVFFI5956RRFZ/), [IGVFFI2976CARS](/sequence-files/IGVFFI2976CARS/), [IGVFFI1594NIYR](/sequence-files/IGVFFI1594NIYR/), [IGVFFI8600XJSP](/sequence-files/IGVFFI8600XJSP/), [IGVFFI2492BPYV](/sequence-files/IGVFFI2492BPYV/), [IGVFFI0662BBNP](/sequence-files/IGVFFI0662BBNP/) 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/IGVFDS0508ERUQ/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4834SKZS/",
"accession": "IGVFDS4834SKZS",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_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": "2023-12-08T23:53:39.445885+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/IGVFFI5956RRFZ/",
"accession": "IGVFFI5956RRFZ",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_exprs_10Xlane2_seqlane1_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:46.213933+00:00",
"file_format": "fastq",
"file_size": 905714526,
"href": "/sequence-files/IGVFFI5956RRFZ/@@download/IGVFFI5956RRFZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/77604437-d54a-41d3-a4eb-26feabd3ca25/IGVFFI5956RRFZ.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/VPR_exprs_2/VPR_exprs_2_S4_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2976CARS/",
"accession": "IGVFFI2976CARS",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_exprs_10Xlane2_seqlane1_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:47.456064+00:00",
"file_format": "fastq",
"file_size": 3085073319,
"href": "/sequence-files/IGVFFI2976CARS/@@download/IGVFFI2976CARS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/410d1d42-1e6c-4747-8bc1-628085469c84/IGVFFI2976CARS.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/VPR_exprs_2/VPR_exprs_2_S4_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1594NIYR/",
"accession": "IGVFFI1594NIYR",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_exprs_10Xlane2_seqlane1_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:48.820852+00:00",
"file_format": "fastq",
"file_size": 6651865973,
"href": "/sequence-files/IGVFFI1594NIYR/@@download/IGVFFI1594NIYR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/5042e86f-7d60-4c69-85d3-88d69e8e1b87/IGVFFI1594NIYR.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/VPR_exprs_2/VPR_exprs_2_S4_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8600XJSP/",
"accession": "IGVFFI8600XJSP",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_exprs_10Xlane2_seqlane2_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:49.965984+00:00",
"file_format": "fastq",
"file_size": 898219571,
"href": "/sequence-files/IGVFFI8600XJSP/@@download/IGVFFI8600XJSP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/3aaef351-29f8-4392-850f-e13a5fad5547/IGVFFI8600XJSP.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/VPR_exprs_2/VPR_exprs_2_S4_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2492BPYV/",
"accession": "IGVFFI2492BPYV",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_exprs_10Xlane2_seqlane2_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:51.174736+00:00",
"file_format": "fastq",
"file_size": 3080601558,
"href": "/sequence-files/IGVFFI2492BPYV/@@download/IGVFFI2492BPYV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/3f8ce523-4fd8-4c9b-ac7f-011b11802f21/IGVFFI2492BPYV.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/VPR_exprs_2/VPR_exprs_2_S4_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0662BBNP/",
"accession": "IGVFFI0662BBNP",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_exprs_10Xlane2_seqlane2_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:52.402823+00:00",
"file_format": "fastq",
"file_size": 6594746294,
"href": "/sequence-files/IGVFFI0662BBNP/@@download/IGVFFI0662BBNP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/43e21c43-631b-4c5d-8893-39eecfc77e22/IGVFFI0662BBNP.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/VPR_exprs_2/VPR_exprs_2_S4_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": "2024-08-13T20:47:08.457646+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9542NUGS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9542NUGS",
"aliases": [
"jay-shendure:CRISPRa_VPR_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/8b61bce4-105c-435e-9b32-1c8903566a9b/",
"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": "2023-12-09T00:50:33.163490+00:00",
"summary": "scCRISPR activation screen integrating a guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci",
"uuid": "0ba1bffe-f4c4-4b58-bbee-170d5734d00d"
}