IGVFDS4502LQQH

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS4502LQQH/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4502LQQH",
    "aliases": [
        "jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane1_CS1"
    ],
    "audit": {
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS4502LQQH](/auxiliary-sets/IGVFDS4502LQQH/) has sequence file(s): [IGVFFI9764UXRA](/sequence-files/IGVFFI9764UXRA/), [IGVFFI7570AUYM](/sequence-files/IGVFFI7570AUYM/), [IGVFFI3927QEMS](/sequence-files/IGVFFI3927QEMS/), [IGVFFI4648IIPG](/sequence-files/IGVFFI4648IIPG/), [IGVFFI3189OKPU](/sequence-files/IGVFFI3189OKPU/), [IGVFFI1733REWQ](/sequence-files/IGVFFI1733REWQ/) 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/IGVFDS4502LQQH/"
            }
        ]
    },
    "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": "2023-12-08T23:52:01.587735+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",
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            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:49:55.134660+00:00",
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            "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_1/VP64_CS1_1_S5_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7570AUYM/",
            "accession": "IGVFFI7570AUYM",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_CS1_10Xlane1_seqlane2_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:49:57.960371+00:00",
            "file_format": "fastq",
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            "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_1/VP64_CS1_1_S5_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3927QEMS/",
            "accession": "IGVFFI3927QEMS",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_CS1_10Xlane1_seqlane2_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:49:59.373909+00:00",
            "file_format": "fastq",
            "file_size": 845945300,
            "href": "/sequence-files/IGVFFI3927QEMS/@@download/IGVFFI3927QEMS.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/1c2a0d2e-19bb-491e-b43f-4b255c740c10/IGVFFI3927QEMS.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_1/VP64_CS1_1_S5_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4648IIPG/",
            "accession": "IGVFFI4648IIPG",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_CS1_10Xlane1_seqlane1_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:49:56.417238+00:00",
            "file_format": "fastq",
            "file_size": 1400676082,
            "href": "/sequence-files/IGVFFI4648IIPG/@@download/IGVFFI4648IIPG.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/9dd11649-644b-40df-9973-3e5fbf9ceba1/IGVFFI4648IIPG.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_1/VP64_CS1_1_S5_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3189OKPU/",
            "accession": "IGVFFI3189OKPU",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_CS1_10Xlane1_seqlane1_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:49:53.541322+00:00",
            "file_format": "fastq",
            "file_size": 289259452,
            "href": "/sequence-files/IGVFFI3189OKPU/@@download/IGVFFI3189OKPU.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/2e64dc30-2b54-40ca-aa1c-ef7c46a7312f/IGVFFI3189OKPU.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_1/VP64_CS1_1_S5_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1733REWQ/",
            "accession": "IGVFFI1733REWQ",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_CS1_10Xlane1_seqlane2_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:00.641697+00:00",
            "file_format": "fastq",
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            "href": "/sequence-files/IGVFFI1733REWQ/@@download/IGVFFI1733REWQ.fastq.gz",
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            "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_1/VP64_CS1_1_S5_L002_R2_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/IGVFDS4863BMGZ/",
            "accession": "IGVFDS4863BMGZ",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane1_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": "2024-08-13T20:47:08.255390+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM4521QSSO/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4521QSSO",
            "aliases": [
                "jay-shendure:CRISPRa_VP64_K562_10Xlane1"
            ],
            "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: 10Xlane1), 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": "2023-12-09T00:49:53.541322+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": "0dc9ea2d-ca73-4152-ba67-3f2d3aedad75"
}