IGVFDS2692VBHQ

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS2692VBHQ/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2692VBHQ",
    "aliases": [
        "gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_LW287"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003660/",
        "status": "released",
        "term_name": "in vitro CRISPR screen using single-cell RNA-seq"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS1937JPZI](/auxiliary-sets/IGVFDS1937JPZI/) has sequence file(s) [IGVFFI8385HABJ](/sequence-files/IGVFFI8385HABJ/), [IGVFFI3275ZEBW](/sequence-files/IGVFFI3275ZEBW/), [IGVFFI1518BMVF](/sequence-files/IGVFFI1518BMVF/), [IGVFFI7286ZUUS](/sequence-files/IGVFFI7286ZUUS/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS1937JPZI/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS1937JPZI](/auxiliary-sets/IGVFDS1937JPZI/) has sequence file(s): [IGVFFI8385HABJ](/sequence-files/IGVFFI8385HABJ/), [IGVFFI3275ZEBW](/sequence-files/IGVFFI3275ZEBW/), [IGVFFI1518BMVF](/sequence-files/IGVFFI1518BMVF/), [IGVFFI7286ZUUS](/sequence-files/IGVFFI7286ZUUS/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_missing_seqspec",
                "path": "/auxiliary-sets/IGVFDS1937JPZI/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS2692VBHQ](/measurement-sets/IGVFDS2692VBHQ/) has sequence file(s) [IGVFFI9530TKDL](/sequence-files/IGVFFI9530TKDL/), [IGVFFI1291VGGB](/sequence-files/IGVFFI1291VGGB/), [IGVFFI8052QAVO](/sequence-files/IGVFFI8052QAVO/), [IGVFFI0588MNHI](/sequence-files/IGVFFI0588MNHI/), [IGVFFI2941KCXR](/sequence-files/IGVFFI2941KCXR/), [IGVFFI8090CHJY](/sequence-files/IGVFFI8090CHJY/), [IGVFFI2261NWNR](/sequence-files/IGVFFI2261NWNR/), [IGVFFI3066OUFL](/sequence-files/IGVFFI3066OUFL/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/measurement-sets/IGVFDS2692VBHQ/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS2692VBHQ](/measurement-sets/IGVFDS2692VBHQ/) has sequence file(s): [IGVFFI9530TKDL](/sequence-files/IGVFFI9530TKDL/), [IGVFFI1291VGGB](/sequence-files/IGVFFI1291VGGB/), [IGVFFI8052QAVO](/sequence-files/IGVFFI8052QAVO/), [IGVFFI0588MNHI](/sequence-files/IGVFFI0588MNHI/), [IGVFFI2941KCXR](/sequence-files/IGVFFI2941KCXR/), [IGVFFI8090CHJY](/sequence-files/IGVFFI8090CHJY/), [IGVFFI2261NWNR](/sequence-files/IGVFFI2261NWNR/), [IGVFFI3066OUFL](/sequence-files/IGVFFI3066OUFL/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_missing_seqspec",
                "path": "/measurement-sets/IGVFDS2692VBHQ/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS2373RGIJ](/auxiliary-sets/IGVFDS2373RGIJ/) has sequence file(s) [IGVFFI7050AVQG](/sequence-files/IGVFFI7050AVQG/), [IGVFFI6282MCFD](/sequence-files/IGVFFI6282MCFD/), [IGVFFI5493BBTV](/sequence-files/IGVFFI5493BBTV/), [IGVFFI1454KXNR](/sequence-files/IGVFFI1454KXNR/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS2373RGIJ/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS2373RGIJ](/auxiliary-sets/IGVFDS2373RGIJ/) has sequence file(s): [IGVFFI7050AVQG](/sequence-files/IGVFFI7050AVQG/), [IGVFFI6282MCFD](/sequence-files/IGVFFI6282MCFD/), [IGVFFI5493BBTV](/sequence-files/IGVFFI5493BBTV/), [IGVFFI1454KXNR](/sequence-files/IGVFFI1454KXNR/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_missing_seqspec",
                "path": "/auxiliary-sets/IGVFDS2373RGIJ/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS1937JPZI/",
            "accession": "IGVFDS1937JPZI",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_sgRNA_LW287"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS2373RGIJ/",
            "accession": "IGVFDS2373RGIJ",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_HTO_LW287"
            ],
            "file_set_type": "cell hashing barcode sequencing",
            "status": "preview"
        }
    ],
    "award": {
        "@id": "/awards/HG011996/",
        "component": "functional characterization",
        "contact_pi": {
            "@id": "/users/95d84f03-8ce0-489c-a755-f33ced139c5d/",
            "title": "Gary Hon"
        },
        "title": "Multiscale functional characterization of genomic variation in human developmental disorders"
    },
    "control_for": [],
    "creation_timestamp": "2024-02-21T21:28:51.084902+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1756PPKO/",
            "accession": "IGVFDO1756PPKO",
            "aliases": [
                "igvf:donor_of_WTC11"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI9530TKDL/",
            "accession": "IGVFFI9530TKDL",
            "aliases": [
                "gary-hon:LW287_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T19:51:35.105818+00:00",
            "file_format": "fastq",
            "file_size": 848056460,
            "href": "/sequence-files/IGVFFI9530TKDL/@@download/IGVFFI9530TKDL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/04/37913b5e-1085-4fb4-869d-28ad3200efe9/IGVFFI9530TKDL.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW287_S2_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1291VGGB/",
            "accession": "IGVFFI1291VGGB",
            "aliases": [
                "gary-hon:LW287_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T19:51:46.412370+00:00",
            "file_format": "fastq",
            "file_size": 950460686,
            "href": "/sequence-files/IGVFFI1291VGGB/@@download/IGVFFI1291VGGB.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/04/d60250b7-0164-4635-9ee3-5d26fb1930b3/IGVFFI1291VGGB.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW287_S2_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8052QAVO/",
            "accession": "IGVFFI8052QAVO",
            "aliases": [
                "gary-hon:LW287_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T19:51:58.445942+00:00",
            "file_format": "fastq",
            "file_size": 3001212186,
            "href": "/sequence-files/IGVFFI8052QAVO/@@download/IGVFFI8052QAVO.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/04/013f6412-7bbb-471d-b336-1584f35160bb/IGVFFI8052QAVO.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW287_S2_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0588MNHI/",
            "accession": "IGVFFI0588MNHI",
            "aliases": [
                "gary-hon:LW287_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T19:52:27.691202+00:00",
            "file_format": "fastq",
            "file_size": 7746113826,
            "href": "/sequence-files/IGVFFI0588MNHI/@@download/IGVFFI0588MNHI.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/04/3e75fa3b-a9f6-4a89-97da-18ffc0efd90c/IGVFFI0588MNHI.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW287_S2_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2941KCXR/",
            "accession": "IGVFFI2941KCXR",
            "aliases": [
                "gary-hon:LW287_2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T19:53:37.580543+00:00",
            "file_format": "fastq",
            "file_size": 796583703,
            "href": "/sequence-files/IGVFFI2941KCXR/@@download/IGVFFI2941KCXR.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/04/6d895ff6-2b06-41f6-9e08-579e3109a041/IGVFFI2941KCXR.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW287_S2_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8090CHJY/",
            "accession": "IGVFFI8090CHJY",
            "aliases": [
                "gary-hon:LW287_2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T19:53:48.396242+00:00",
            "file_format": "fastq",
            "file_size": 880176910,
            "href": "/sequence-files/IGVFFI8090CHJY/@@download/IGVFFI8090CHJY.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/04/cae15c23-4a16-4d01-bf33-77b73c894baf/IGVFFI8090CHJY.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW287_S2_L002_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2261NWNR/",
            "accession": "IGVFFI2261NWNR",
            "aliases": [
                "gary-hon:LW287_2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T19:53:59.814668+00:00",
            "file_format": "fastq",
            "file_size": 2739532382,
            "href": "/sequence-files/IGVFFI2261NWNR/@@download/IGVFFI2261NWNR.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/04/a6b8d1de-c0af-43f9-a21d-c1f76804a344/IGVFFI2261NWNR.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW287_S2_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3066OUFL/",
            "accession": "IGVFFI3066OUFL",
            "aliases": [
                "gary-hon:LW287_2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-04T19:54:26.962640+00:00",
            "file_format": "fastq",
            "file_size": 7068081111,
            "href": "/sequence-files/IGVFFI3066OUFL/@@download/IGVFFI3066OUFL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/04/e73f09ca-b168-4b4a-b865-7cb9bc971193/IGVFFI3066OUFL.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0010963/",
                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW287_S2_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS7340YDHF/"
    ],
    "lab": {
        "@id": "/labs/gary-hon/",
        "title": "Gary Hon, UT"
    },
    "preferred_assay_title": "Perturb-seq",
    "protocols": [
        "https://www.protocols.io/view/experimental-procedures-for-tf-perturb-seq-ut-sout-denf3dbn"
    ],
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM1153INDY/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM1153INDY",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW287"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS2302LCEO/",
                    "accession": "IGVFDS2302LCEO",
                    "file_set_type": "guide library",
                    "status": "preview",
                    "summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
                }
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
                    "modality": "interference",
                    "status": "preview"
                }
            ],
            "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": "preview",
            "summary": "GM25256 (WTC-11) cell line (cellular sub pool: subpool_LW287), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "23",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
        "title": "Mpathi Nzima"
    },
    "submitted_files_timestamp": "2024-03-04T19:51:35.105818+00:00",
    "submitter_comment": "Transcriptiome for LW287",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "b7e426f1-2366-4598-8009-1993c34e1c20"
}