IGVFDS5033OBAO

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS5033OBAO/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5033OBAO",
    "aliases": [
        "gary-hon:CM_Pilot_2_Lenti_RNA_LW265"
    ],
    "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": "Measurement set [IGVFDS5033OBAO](/measurement-sets/IGVFDS5033OBAO/) has sequence file(s) [IGVFFI5312MTPV](/sequence-files/IGVFFI5312MTPV/), [IGVFFI0514WTDY](/sequence-files/IGVFFI0514WTDY/), [IGVFFI7590TIFL](/sequence-files/IGVFFI7590TIFL/), [IGVFFI3835WKIZ](/sequence-files/IGVFFI3835WKIZ/), [IGVFFI8436EDEK](/sequence-files/IGVFFI8436EDEK/), [IGVFFI9055CJNY](/sequence-files/IGVFFI9055CJNY/), [IGVFFI9909EVUS](/sequence-files/IGVFFI9909EVUS/), [IGVFFI1034SQQC](/sequence-files/IGVFFI1034SQQC/) 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/IGVFDS5033OBAO/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS5033OBAO](/measurement-sets/IGVFDS5033OBAO/) has sequence file(s): [IGVFFI5312MTPV](/sequence-files/IGVFFI5312MTPV/), [IGVFFI0514WTDY](/sequence-files/IGVFFI0514WTDY/), [IGVFFI7590TIFL](/sequence-files/IGVFFI7590TIFL/), [IGVFFI3835WKIZ](/sequence-files/IGVFFI3835WKIZ/), [IGVFFI8436EDEK](/sequence-files/IGVFFI8436EDEK/), [IGVFFI9055CJNY](/sequence-files/IGVFFI9055CJNY/), [IGVFFI9909EVUS](/sequence-files/IGVFFI9909EVUS/), [IGVFFI1034SQQC](/sequence-files/IGVFFI1034SQQC/) 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/IGVFDS5033OBAO/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS3633OXMI](/auxiliary-sets/IGVFDS3633OXMI/) has sequence file(s) [IGVFFI6653WHJW](/sequence-files/IGVFFI6653WHJW/), [IGVFFI4629JAWT](/sequence-files/IGVFFI4629JAWT/), [IGVFFI9092WARW](/sequence-files/IGVFFI9092WARW/), [IGVFFI6791VIRM](/sequence-files/IGVFFI6791VIRM/) 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/IGVFDS3633OXMI/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS3633OXMI](/auxiliary-sets/IGVFDS3633OXMI/) has sequence file(s): [IGVFFI6653WHJW](/sequence-files/IGVFFI6653WHJW/), [IGVFFI4629JAWT](/sequence-files/IGVFFI4629JAWT/), [IGVFFI9092WARW](/sequence-files/IGVFFI9092WARW/), [IGVFFI6791VIRM](/sequence-files/IGVFFI6791VIRM/) 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/IGVFDS3633OXMI/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS7126MOZN](/auxiliary-sets/IGVFDS7126MOZN/) has sequence file(s) [IGVFFI9073DXNX](/sequence-files/IGVFFI9073DXNX/), [IGVFFI4148SPYG](/sequence-files/IGVFFI4148SPYG/), [IGVFFI0764VODB](/sequence-files/IGVFFI0764VODB/), [IGVFFI2927WRJG](/sequence-files/IGVFFI2927WRJG/) 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/IGVFDS7126MOZN/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS7126MOZN](/auxiliary-sets/IGVFDS7126MOZN/) has sequence file(s): [IGVFFI9073DXNX](/sequence-files/IGVFFI9073DXNX/), [IGVFFI4148SPYG](/sequence-files/IGVFFI4148SPYG/), [IGVFFI0764VODB](/sequence-files/IGVFFI0764VODB/), [IGVFFI2927WRJG](/sequence-files/IGVFFI2927WRJG/) 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/IGVFDS7126MOZN/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS3633OXMI/",
            "accession": "IGVFDS3633OXMI",
            "aliases": [
                "gary-hon:CM_Pilot_2_Lenti_HTO_LW265"
            ],
            "file_set_type": "cell hashing barcode sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS7126MOZN/",
            "accession": "IGVFDS7126MOZN",
            "aliases": [
                "gary-hon:CM_Pilot_2_Lenti_sgRNA_LW265"
            ],
            "file_set_type": "gRNA 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": "2024-02-15T23:43:24.898375+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": [
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            "@id": "/sequence-files/IGVFFI5312MTPV/",
            "accession": "IGVFFI5312MTPV",
            "aliases": [
                "gary-hon:LW265_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:57:52.383323+00:00",
            "file_format": "fastq",
            "file_size": 1846827070,
            "href": "/sequence-files/IGVFFI5312MTPV/@@download/IGVFFI5312MTPV.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/9dc11a56-a199-4897-be23-c9adae74f772/IGVFFI5312MTPV.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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW265_S5_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0514WTDY/",
            "accession": "IGVFFI0514WTDY",
            "aliases": [
                "gary-hon:LW265_2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:59:18.540863+00:00",
            "file_format": "fastq",
            "file_size": 1722033058,
            "href": "/sequence-files/IGVFFI0514WTDY/@@download/IGVFFI0514WTDY.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/64dbb133-7621-4d00-9735-9a02c6e686be/IGVFFI0514WTDY.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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW265_S5_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7590TIFL/",
            "accession": "IGVFFI7590TIFL",
            "aliases": [
                "gary-hon:LW265_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:58:12.238564+00:00",
            "file_format": "fastq",
            "file_size": 4581960740,
            "href": "/sequence-files/IGVFFI7590TIFL/@@download/IGVFFI7590TIFL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/95cf687a-00de-47b6-9ca3-1d0ac1ed992a/IGVFFI7590TIFL.fastq.gz",
            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NextSeq 2000"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW265_S5_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3835WKIZ/",
            "accession": "IGVFFI3835WKIZ",
            "aliases": [
                "gary-hon:LW265_2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:59:37.465795+00:00",
            "file_format": "fastq",
            "file_size": 4356626782,
            "href": "/sequence-files/IGVFFI3835WKIZ/@@download/IGVFFI3835WKIZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/8dc1876b-a19b-4e7a-a8de-96a8f7498b54/IGVFFI3835WKIZ.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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW265_S5_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8436EDEK/",
            "accession": "IGVFFI8436EDEK",
            "aliases": [
                "gary-hon:LW265_2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:58:56.722926+00:00",
            "file_format": "fastq",
            "file_size": 565122871,
            "href": "/sequence-files/IGVFFI8436EDEK/@@download/IGVFFI8436EDEK.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/77c55770-eb5e-4f50-8644-7af01a8a8433/IGVFFI8436EDEK.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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW265_S5_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9055CJNY/",
            "accession": "IGVFFI9055CJNY",
            "aliases": [
                "gary-hon:LW265_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:57:33.637951+00:00",
            "file_format": "fastq",
            "file_size": 587458313,
            "href": "/sequence-files/IGVFFI9055CJNY/@@download/IGVFFI9055CJNY.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/3570388e-8fe5-476e-9c82-6147cb8f95cb/IGVFFI9055CJNY.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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW265_S5_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9909EVUS/",
            "accession": "IGVFFI9909EVUS",
            "aliases": [
                "gary-hon:LW265_2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:59:09.360358+00:00",
            "file_format": "fastq",
            "file_size": 566558677,
            "href": "/sequence-files/IGVFFI9909EVUS/@@download/IGVFFI9909EVUS.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/02/20/88d7a06b-68f8-4e78-a1d9-11950de148f3/IGVFFI9909EVUS.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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW265_S5_L002_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1034SQQC/",
            "accession": "IGVFFI1034SQQC",
            "aliases": [
                "gary-hon:LW265_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-02-20T17:57:43.030091+00:00",
            "file_format": "fastq",
            "file_size": 613602189,
            "href": "/sequence-files/IGVFFI1034SQQC/@@download/IGVFFI1034SQQC.fastq.gz",
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            "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/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW265_S5_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS4003HZAB/"
    ],
    "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/IGVFSM7215JDPM/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7215JDPM",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW265"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS9629YZLO/",
                    "accession": "IGVFDS9629YZLO",
                    "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) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW265), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000746/",
                "status": "released",
                "term_name": "cardiac muscle cell"
            },
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "23",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
        "title": "Mpathi Nzima"
    },
    "submitted_files_timestamp": "2024-02-20T17:57:33.637951+00:00",
    "submitter_comment": "Transcriptiome for LW265'",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "7d999a47-35a2-4cff-8866-99dc93d29a8c"
}