IGVFDS5502LTCL

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS5502LTCL/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5502LTCL",
    "aliases": [
        "gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_LW431"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003660/",
        "status": "released",
        "term_name": "in vitro CRISPR screen using single-cell RNA-seq"
    },
    "audit": {
        "ERROR": [
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS1182KBMU](/auxiliary-sets/IGVFDS1182KBMU/) has a sequence file [IGVFFI6583VNDG](/sequence-files/IGVFFI6583VNDG/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS1182KBMU/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS1182KBMU](/auxiliary-sets/IGVFDS1182KBMU/) has a sequence file [IGVFFI9145LELN](/sequence-files/IGVFFI9145LELN/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS1182KBMU/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS1182KBMU](/auxiliary-sets/IGVFDS1182KBMU/) has a sequence file [IGVFFI1005GDSX](/sequence-files/IGVFFI1005GDSX/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS1182KBMU/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS1182KBMU](/auxiliary-sets/IGVFDS1182KBMU/) has a sequence file [IGVFFI0606VNOW](/sequence-files/IGVFFI0606VNOW/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS1182KBMU/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS2275IPCJ](/auxiliary-sets/IGVFDS2275IPCJ/) has a sequence file [IGVFFI8808EXTD](/sequence-files/IGVFFI8808EXTD/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS2275IPCJ/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS2275IPCJ](/auxiliary-sets/IGVFDS2275IPCJ/) has a sequence file [IGVFFI4737ARVA](/sequence-files/IGVFFI4737ARVA/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS2275IPCJ/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS2275IPCJ](/auxiliary-sets/IGVFDS2275IPCJ/) has a sequence file [IGVFFI6041NQVA](/sequence-files/IGVFFI6041NQVA/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS2275IPCJ/"
            },
            {
                "category": "inconsistent sequencing kit",
                "detail": "Auxiliary set [IGVFDS2275IPCJ](/auxiliary-sets/IGVFDS2275IPCJ/) has a sequence file [IGVFFI3054WXFJ](/sequence-files/IGVFFI3054WXFJ/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
                "level": 60,
                "level_name": "ERROR",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS2275IPCJ/"
            }
        ],
        "INTERNAL_ACTION": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS1182KBMU](/auxiliary-sets/IGVFDS1182KBMU/) has sequence file(s): [IGVFFI6583VNDG](/sequence-files/IGVFFI6583VNDG/), [IGVFFI9145LELN](/sequence-files/IGVFFI9145LELN/), [IGVFFI1005GDSX](/sequence-files/IGVFFI1005GDSX/), [IGVFFI0606VNOW](/sequence-files/IGVFFI0606VNOW/) 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/IGVFDS1182KBMU/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS2275IPCJ](/auxiliary-sets/IGVFDS2275IPCJ/) has sequence file(s): [IGVFFI8808EXTD](/sequence-files/IGVFFI8808EXTD/), [IGVFFI4737ARVA](/sequence-files/IGVFFI4737ARVA/), [IGVFFI6041NQVA](/sequence-files/IGVFFI6041NQVA/), [IGVFFI3054WXFJ](/sequence-files/IGVFFI3054WXFJ/) 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/IGVFDS2275IPCJ/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS5502LTCL](/measurement-sets/IGVFDS5502LTCL/) has sequence file(s): [IGVFFI4784TVQJ](/sequence-files/IGVFFI4784TVQJ/), [IGVFFI7003PLXM](/sequence-files/IGVFFI7003PLXM/), [IGVFFI3941NWZZ](/sequence-files/IGVFFI3941NWZZ/), [IGVFFI3988NDQI](/sequence-files/IGVFFI3988NDQI/) 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/IGVFDS5502LTCL/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS1182KBMU/",
            "accession": "IGVFDS1182KBMU",
            "aliases": [
                "gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_sgRNA_LW431"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS2275IPCJ/",
            "accession": "IGVFDS2275IPCJ",
            "aliases": [
                "gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_HTO_LW431"
            ],
            "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": "2024-08-16T20:32:04.081618+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO2718IDDQ/",
            "accession": "IGVFDO2718IDDQ",
            "aliases": [
                "igvf:donor_of_H9"
            ],
            "sex": "female",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI4784TVQJ/",
            "accession": "IGVFFI4784TVQJ",
            "aliases": [
                "gary-hon:LW431_4_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-13T19:02:22.481147+00:00",
            "file_format": "fastq",
            "file_size": 37741742748,
            "href": "/sequence-files/IGVFFI4784TVQJ/@@download/IGVFFI4784TVQJ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/13/a3736b6f-1be9-4e42-8ab7-97e606d2a494/IGVFFI4784TVQJ.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022841/",
                "status": "released",
                "term_name": "Illumina NovaSeq X Plus"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon17_18/scRNA//LW431_S7_L004_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7003PLXM/",
            "accession": "IGVFFI7003PLXM",
            "aliases": [
                "gary-hon:LW431_4_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-13T18:55:35.484385+00:00",
            "file_format": "fastq",
            "file_size": 3014348332,
            "href": "/sequence-files/IGVFFI7003PLXM/@@download/IGVFFI7003PLXM.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/13/ed6b4c76-9e61-4ba4-a290-26b50989a837/IGVFFI7003PLXM.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022841/",
                "status": "released",
                "term_name": "Illumina NovaSeq X Plus"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon17_18/scRNA//LW431_S7_L004_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3941NWZZ/",
            "accession": "IGVFFI3941NWZZ",
            "aliases": [
                "gary-hon:LW431_4_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-13T18:56:11.420288+00:00",
            "file_format": "fastq",
            "file_size": 2829899521,
            "href": "/sequence-files/IGVFFI3941NWZZ/@@download/IGVFFI3941NWZZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/13/671d3165-3a30-405f-abaf-46ad2dffc4e9/IGVFFI3941NWZZ.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022841/",
                "status": "released",
                "term_name": "Illumina NovaSeq X Plus"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon17_18/scRNA//LW431_S7_L004_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3988NDQI/",
            "accession": "IGVFFI3988NDQI",
            "aliases": [
                "gary-hon:LW431_4_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-13T18:56:46.580312+00:00",
            "file_format": "fastq",
            "file_size": 37490399513,
            "href": "/sequence-files/IGVFFI3988NDQI/@@download/IGVFFI3988NDQI.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/13/9c21a19f-e9a9-4337-b346-6d2d36e4e641/IGVFFI3988NDQI.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022841/",
                "status": "released",
                "term_name": "Illumina NovaSeq X Plus"
            },
            "status": "preview",
            "submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon17_18/scRNA//LW431_S7_L004_R1_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS2266YDVM/"
    ],
    "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/IGVFSM5829AVCL/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM5829AVCL",
            "aliases": [
                "nikhil-munshi:differentited_H9_CM_Pilot2_Mini_PB9_LW431"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS0346MQBH/",
                    "accession": "IGVFDS0346MQBH",
                    "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_0003045/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:H9"
                    ],
                    "status": "released",
                    "summary": "H9",
                    "term_name": "H9"
                }
            ],
            "status": "preview",
            "summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW431), female, Homo sapiens modified with CRISPRi Sp-dCas9, transfected 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": "2024-11-13T18:46:19.557880+00:00",
    "submitter_comment": "Transcriptiome for LW431",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "996c6339-cb2d-4cc0-a783-94c475fd0382"
}