IGVFDS8929VNCP

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS8929VNCP/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS8929VNCP",
    "aliases": [
        "jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane2_CS1"
    ],
    "audit": {
        "NOT_COMPLIANT": [
            {
                "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/"
            }
        ]
    },
    "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": "2023-12-08T23:52:02.733833+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO9208RPQQ/",
            "accession": "IGVFDO9208RPQQ",
            "aliases": [
                "igvf:donor_of_K562"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "gRNA sequencing",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI6893EPCL/",
            "accession": "IGVFFI6893EPCL",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_CS1_10Xlane2_seqlane1_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:04.406166+00:00",
            "file_format": "fastq",
            "file_size": 1367803313,
            "href": "/sequence-files/IGVFFI6893EPCL/@@download/IGVFFI6893EPCL.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/4c35886d-4ad6-4363-97a2-c292507bf2f3/IGVFFI6893EPCL.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "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_CS1_2/VP64_CS1_2_S6_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0355AKWQ/",
            "accession": "IGVFFI0355AKWQ",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_CS1_10Xlane2_seqlane2_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:05.892301+00:00",
            "file_format": "fastq",
            "file_size": 275553789,
            "href": "/sequence-files/IGVFFI0355AKWQ/@@download/IGVFFI0355AKWQ.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/c51f807c-7013-4536-a4bf-89263148e908/IGVFFI0355AKWQ.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "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_CS1_2/VP64_CS1_2_S6_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7148JTBN/",
            "accession": "IGVFFI7148JTBN",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_CS1_10Xlane2_seqlane2_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:08.356288+00:00",
            "file_format": "fastq",
            "file_size": 1317764391,
            "href": "/sequence-files/IGVFFI7148JTBN/@@download/IGVFFI7148JTBN.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/9c511f18-90b5-47e6-bb95-0ade66dd670d/IGVFFI7148JTBN.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "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_CS1_2/VP64_CS1_2_S6_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5295OHTL/",
            "accession": "IGVFFI5295OHTL",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_CS1_10Xlane2_seqlane1_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:01.911165+00:00",
            "file_format": "fastq",
            "file_size": 285795540,
            "href": "/sequence-files/IGVFFI5295OHTL/@@download/IGVFFI5295OHTL.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/fff0dddf-1a6c-464d-9f5b-5df7100b12c3/IGVFFI5295OHTL.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "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_CS1_2/VP64_CS1_2_S6_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3658HZBE/",
            "accession": "IGVFFI3658HZBE",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_CS1_10Xlane2_seqlane1_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:02.987891+00:00",
            "file_format": "fastq",
            "file_size": 892252479,
            "href": "/sequence-files/IGVFFI3658HZBE/@@download/IGVFFI3658HZBE.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/f6ba8f4f-3549-4cce-867b-5ac7f1500340/IGVFFI3658HZBE.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "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_CS1_2/VP64_CS1_2_S6_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0332PBFZ/",
            "accession": "IGVFFI0332PBFZ",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_CS1_10Xlane2_seqlane2_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:07.151971+00:00",
            "file_format": "fastq",
            "file_size": 855119382,
            "href": "/sequence-files/IGVFFI0332PBFZ/@@download/IGVFFI0332PBFZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/2ea9f8be-a4c7-4413-aaec-04d5aaef0c00/IGVFFI0332PBFZ.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "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_CS1_2/VP64_CS1_2_S6_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_file_set_for": [
        "/analysis-sets/IGVFDS9078ZWQH/"
    ],
    "lab": {
        "@id": "/labs/jay-shendure/",
        "title": "Jay Shendure, UW"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS8535CXVX/",
            "accession": "IGVFDS8535CXVX",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane2_exprs"
            ],
            "preferred_assay_title": "scCRISPR screen"
        }
    ],
    "publications": [
        {
            "@id": "/publications/20fcbdbb-5a47-41c6-b80b-e6dd0e8a8d3e/",
            "publication_identifiers": [
                "doi:10.1101/2023.03.28.534017"
            ]
        }
    ],
    "release_timestamp": "2024-08-13T20:47:07.766315+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": [
                "/construct-library-sets/IGVFDS7581DNXF/"
            ],
            "modifications": [
                "/crispr-modifications/ee99bf66-2a5a-4ec6-8380-9434b259afd1/"
            ],
            "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": "11",
    "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": "gRNA sequencing for scCRISPR activation screen integrating a guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci",
    "uuid": "221867df-7fce-4848-bca9-314e60e2d26c"
}