IGVFDS2220HHTN

released
{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS2220HHTN/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2220HHTN",
    "aliases": [
        "jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane2_CS1"
    ],
    "audit": {
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS2220HHTN](/auxiliary-sets/IGVFDS2220HHTN/) has sequence file(s): [IGVFFI4137IEHI](/sequence-files/IGVFFI4137IEHI/), [IGVFFI4398ITZJ](/sequence-files/IGVFFI4398ITZJ/), [IGVFFI4961EMLW](/sequence-files/IGVFFI4961EMLW/), [IGVFFI7687RJYL](/sequence-files/IGVFFI7687RJYL/), [IGVFFI7842UOGS](/sequence-files/IGVFFI7842UOGS/), [IGVFFI4732FLWG](/sequence-files/IGVFFI4732FLWG/), [IGVFFI8008YPNQ](/sequence-files/IGVFFI8008YPNQ/), [IGVFFI0849UBQW](/sequence-files/IGVFFI0849UBQW/) 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/IGVFDS2220HHTN/"
            }
        ]
    },
    "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": "2023-12-08T23:52:06.493785+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1756PPKO/",
            "accession": "IGVFDO1756PPKO",
            "aliases": [
                "igvf:donor_of_WTC11"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "gRNA sequencing",
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            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane2_seqlane2_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:51:08.665756+00:00",
            "file_format": "fastq",
            "file_size": 313646402,
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            "s3_uri": "s3://igvf-files/2023/12/09/6bd74b50-22dc-43ad-afa6-204f7b06a03c/IGVFFI4137IEHI.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_2/CS1_2_S6_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4398ITZJ/",
            "accession": "IGVFFI4398ITZJ",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane2_seqlane2_I2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:51:09.759013+00:00",
            "file_format": "fastq",
            "file_size": 325685618,
            "href": "/sequence-files/IGVFFI4398ITZJ/@@download/IGVFFI4398ITZJ.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/f00ee4f0-9b53-4e92-b714-c7ff74ec965f/IGVFFI4398ITZJ.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_2/CS1_2_S6_L002_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4961EMLW/",
            "accession": "IGVFFI4961EMLW",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane2_seqlane2_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:51:10.826415+00:00",
            "file_format": "fastq",
            "file_size": 1025441103,
            "href": "/sequence-files/IGVFFI4961EMLW/@@download/IGVFFI4961EMLW.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/af4a9569-1765-497c-a0a3-f187cf840484/IGVFFI4961EMLW.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_2/CS1_2_S6_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7687RJYL/",
            "accession": "IGVFFI7687RJYL",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane2_seqlane2_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:51:11.951900+00:00",
            "file_format": "fastq",
            "file_size": 1210639966,
            "href": "/sequence-files/IGVFFI7687RJYL/@@download/IGVFFI7687RJYL.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/10b76cb9-6d60-4c86-9dec-f3d977eb7c4d/IGVFFI7687RJYL.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_2/CS1_2_S6_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7842UOGS/",
            "accession": "IGVFFI7842UOGS",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane2_seqlane1_I2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:51:04.952717+00:00",
            "file_format": "fastq",
            "file_size": 347022015,
            "href": "/sequence-files/IGVFFI7842UOGS/@@download/IGVFFI7842UOGS.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/6e9c2aa1-ffc5-4223-9b41-19ec31f37f72/IGVFFI7842UOGS.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_2/CS1_2_S6_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4732FLWG/",
            "accession": "IGVFFI4732FLWG",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane2_seqlane1_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:51:07.635031+00:00",
            "file_format": "fastq",
            "file_size": 1292079567,
            "href": "/sequence-files/IGVFFI4732FLWG/@@download/IGVFFI4732FLWG.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/ebc785a9-aa40-4a58-a9aa-5fbf5b644680/IGVFFI4732FLWG.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_2/CS1_2_S6_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8008YPNQ/",
            "accession": "IGVFFI8008YPNQ",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane2_seqlane1_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:51:03.848506+00:00",
            "file_format": "fastq",
            "file_size": 322906507,
            "href": "/sequence-files/IGVFFI8008YPNQ/@@download/IGVFFI8008YPNQ.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/53cf9d9c-8755-43be-9049-a9301221f5d6/IGVFFI8008YPNQ.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_2/CS1_2_S6_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0849UBQW/",
            "accession": "IGVFFI0849UBQW",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane2_seqlane1_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-09T00:51:06.382739+00:00",
            "file_format": "fastq",
            "file_size": 1087405542,
            "href": "/sequence-files/IGVFFI0849UBQW/@@download/IGVFFI0849UBQW.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/09/595f6068-1d9c-4cd5-8d8c-86b0c7688cff/IGVFFI0849UBQW.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0010963/",
            "submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_2/CS1_2_S6_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_file_set_for": [
        "/analysis-sets/IGVFDS4021XJLW/"
    ],
    "lab": {
        "@id": "/labs/jay-shendure/",
        "title": "Jay Shendure, UW"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS0272VVTX/",
            "accession": "IGVFDS0272VVTX",
            "aliases": [
                "jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_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": "2024-08-13T20:47:22.455248+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM9913PXTT/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9913PXTT",
            "aliases": [
                "jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane2"
            ],
            "cell_fate_change_treatments": [
                "/treatments/13a2bfe2-9124-4254-b0fe-8c221077201f/"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS7581DNXF/"
            ],
            "modifications": [
                "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/"
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0009747/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:WTC11"
                    ],
                    "status": "released",
                    "summary": "GM25256 (WTC-11)",
                    "term_name": "GM25256 (WTC-11)"
                }
            ],
            "status": "released",
            "summary": "GM25256 (WTC-11) differentiated cell specimen induced to neuron for 19 days (cellular sub pool: 10Xlane2), male, Homo sapiens modified with a guide library",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000540/",
                "term_name": "neuron"
            },
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "11",
    "status": "released",
    "submitted_by": {
        "@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
        "title": "Beth Martin"
    },
    "submitted_files_timestamp": "2023-12-09T00:51:03.848506+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": "5cb44b8e-6570-45af-9bf6-4cdf9c01423c"
}