IGVFDS4621HUKP

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS4621HUKP/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4621HUKP",
    "aliases": [
        "jay-shendure:CRISPRa_singlecell_K562_VPR_10Xlane1_CS1"
    ],
    "audit": {
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS4621HUKP](/auxiliary-sets/IGVFDS4621HUKP/) has sequence file(s): [IGVFFI1163CNBZ](/sequence-files/IGVFFI1163CNBZ/), [IGVFFI3887HQZR](/sequence-files/IGVFFI3887HQZR/), [IGVFFI3175HZHT](/sequence-files/IGVFFI3175HZHT/), [IGVFFI5218FTCG](/sequence-files/IGVFFI5218FTCG/), [IGVFFI7439CGLC](/sequence-files/IGVFFI7439CGLC/), [IGVFFI2138EWHH](/sequence-files/IGVFFI2138EWHH/) 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/IGVFDS4621HUKP/"
            }
        ]
    },
    "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": "2023-12-08T23:52:03.799708+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/IGVFFI1163CNBZ/",
            "accession": "IGVFFI1163CNBZ",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_CS1_10Xlane1_seqlane2_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:30.620375+00:00",
            "file_format": "fastq",
            "file_size": 756501538,
            "href": "/sequence-files/IGVFFI1163CNBZ/@@download/IGVFFI1163CNBZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/20be1025-ee0b-4031-92bb-0a19e502e155/IGVFFI1163CNBZ.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/VPR_CS1_1/VPR_CS1_1_S7_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3887HQZR/",
            "accession": "IGVFFI3887HQZR",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_CS1_10Xlane1_seqlane1_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:25.812810+00:00",
            "file_format": "fastq",
            "file_size": 288516137,
            "href": "/sequence-files/IGVFFI3887HQZR/@@download/IGVFFI3887HQZR.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/1add7622-1f58-4a29-aca7-32c29a1224a2/IGVFFI3887HQZR.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/VPR_CS1_1/VPR_CS1_1_S7_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3175HZHT/",
            "accession": "IGVFFI3175HZHT",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_CS1_10Xlane1_seqlane1_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:26.908292+00:00",
            "file_format": "fastq",
            "file_size": 794850789,
            "href": "/sequence-files/IGVFFI3175HZHT/@@download/IGVFFI3175HZHT.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/4355b444-271d-43c7-b814-a9bf410311a7/IGVFFI3175HZHT.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/VPR_CS1_1/VPR_CS1_1_S7_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5218FTCG/",
            "accession": "IGVFFI5218FTCG",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_CS1_10Xlane1_seqlane1_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:28.008887+00:00",
            "file_format": "fastq",
            "file_size": 1404831584,
            "href": "/sequence-files/IGVFFI5218FTCG/@@download/IGVFFI5218FTCG.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/cafd3f64-6cb4-4968-8123-295ccbbccdef/IGVFFI5218FTCG.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/VPR_CS1_1/VPR_CS1_1_S7_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7439CGLC/",
            "accession": "IGVFFI7439CGLC",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_CS1_10Xlane1_seqlane2_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:29.103903+00:00",
            "file_format": "fastq",
            "file_size": 274454086,
            "href": "/sequence-files/IGVFFI7439CGLC/@@download/IGVFFI7439CGLC.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/2e86eddc-98ed-4520-986d-4290a8f253b8/IGVFFI7439CGLC.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/VPR_CS1_1/VPR_CS1_1_S7_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2138EWHH/",
            "accession": "IGVFFI2138EWHH",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_CS1_10Xlane1_seqlane2_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:50:32.109863+00:00",
            "file_format": "fastq",
            "file_size": 1353556483,
            "href": "/sequence-files/IGVFFI2138EWHH/@@download/IGVFFI2138EWHH.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/VPR_CS1_1/VPR_CS1_1_S7_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/IGVFDS7395DPAD/",
            "accession": "IGVFDS7395DPAD",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_K562_VPR_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": "2024-08-13T20:47:07.018575+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM1594ZOQH/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM1594ZOQH",
            "aliases": [
                "jay-shendure:CRISPRa_VPR_K562_10Xlane1"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS7581DNXF/"
            ],
            "modifications": [
                "/crispr-modifications/8b61bce4-105c-435e-9b32-1c8903566a9b/"
            ],
            "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": "2023-12-09T00:50:25.812810+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": "9a2a01ab-50e6-49d4-9f27-e9b6b6710896"
}