IGVFDS2143BSOH

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS2143BSOH/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2143BSOH",
    "aliases": [
        "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW281"
    ],
    "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 [IGVFDS2143BSOH](/measurement-sets/IGVFDS2143BSOH/) has sequence file(s) [IGVFFI6060RUDC](/sequence-files/IGVFFI6060RUDC/), [IGVFFI1727DJMY](/sequence-files/IGVFFI1727DJMY/), [IGVFFI5007DWHI](/sequence-files/IGVFFI5007DWHI/), [IGVFFI9041LHWG](/sequence-files/IGVFFI9041LHWG/), [IGVFFI7614TPCO](/sequence-files/IGVFFI7614TPCO/), [IGVFFI6389SAKA](/sequence-files/IGVFFI6389SAKA/), [IGVFFI6933IHKQ](/sequence-files/IGVFFI6933IHKQ/), [IGVFFI0239MXTR](/sequence-files/IGVFFI0239MXTR/) 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/IGVFDS2143BSOH/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS2143BSOH](/measurement-sets/IGVFDS2143BSOH/) has sequence file(s): [IGVFFI6060RUDC](/sequence-files/IGVFFI6060RUDC/), [IGVFFI1727DJMY](/sequence-files/IGVFFI1727DJMY/), [IGVFFI5007DWHI](/sequence-files/IGVFFI5007DWHI/), [IGVFFI9041LHWG](/sequence-files/IGVFFI9041LHWG/), [IGVFFI7614TPCO](/sequence-files/IGVFFI7614TPCO/), [IGVFFI6389SAKA](/sequence-files/IGVFFI6389SAKA/), [IGVFFI6933IHKQ](/sequence-files/IGVFFI6933IHKQ/), [IGVFFI0239MXTR](/sequence-files/IGVFFI0239MXTR/) 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/IGVFDS2143BSOH/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS2612LSTD](/auxiliary-sets/IGVFDS2612LSTD/) has sequence file(s) [IGVFFI6611BGPK](/sequence-files/IGVFFI6611BGPK/), [IGVFFI4582VNCZ](/sequence-files/IGVFFI4582VNCZ/), [IGVFFI1807ZQQP](/sequence-files/IGVFFI1807ZQQP/), [IGVFFI6515ZKTF](/sequence-files/IGVFFI6515ZKTF/), [IGVFFI4919JJPZ](/sequence-files/IGVFFI4919JJPZ/), [IGVFFI8349NVKT](/sequence-files/IGVFFI8349NVKT/), [IGVFFI5164GGZB](/sequence-files/IGVFFI5164GGZB/), [IGVFFI4061QSKL](/sequence-files/IGVFFI4061QSKL/) 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/IGVFDS2612LSTD/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS2612LSTD](/auxiliary-sets/IGVFDS2612LSTD/) has sequence file(s): [IGVFFI6611BGPK](/sequence-files/IGVFFI6611BGPK/), [IGVFFI4582VNCZ](/sequence-files/IGVFFI4582VNCZ/), [IGVFFI1807ZQQP](/sequence-files/IGVFFI1807ZQQP/), [IGVFFI6515ZKTF](/sequence-files/IGVFFI6515ZKTF/), [IGVFFI4919JJPZ](/sequence-files/IGVFFI4919JJPZ/), [IGVFFI8349NVKT](/sequence-files/IGVFFI8349NVKT/), [IGVFFI5164GGZB](/sequence-files/IGVFFI5164GGZB/), [IGVFFI4061QSKL](/sequence-files/IGVFFI4061QSKL/) 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/IGVFDS2612LSTD/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS2549GCKW](/auxiliary-sets/IGVFDS2549GCKW/) has sequence file(s) [IGVFFI4327UMKJ](/sequence-files/IGVFFI4327UMKJ/), [IGVFFI3275IUJQ](/sequence-files/IGVFFI3275IUJQ/), [IGVFFI0782ZJOJ](/sequence-files/IGVFFI0782ZJOJ/), [IGVFFI0713WITI](/sequence-files/IGVFFI0713WITI/), [IGVFFI4515BKOL](/sequence-files/IGVFFI4515BKOL/), [IGVFFI2642JAIF](/sequence-files/IGVFFI2642JAIF/), [IGVFFI8312SSMA](/sequence-files/IGVFFI8312SSMA/), [IGVFFI5462TUJG](/sequence-files/IGVFFI5462TUJG/) 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/IGVFDS2549GCKW/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS2549GCKW](/auxiliary-sets/IGVFDS2549GCKW/) has sequence file(s): [IGVFFI4327UMKJ](/sequence-files/IGVFFI4327UMKJ/), [IGVFFI3275IUJQ](/sequence-files/IGVFFI3275IUJQ/), [IGVFFI0782ZJOJ](/sequence-files/IGVFFI0782ZJOJ/), [IGVFFI0713WITI](/sequence-files/IGVFFI0713WITI/), [IGVFFI4515BKOL](/sequence-files/IGVFFI4515BKOL/), [IGVFFI2642JAIF](/sequence-files/IGVFFI2642JAIF/), [IGVFFI8312SSMA](/sequence-files/IGVFFI8312SSMA/), [IGVFFI5462TUJG](/sequence-files/IGVFFI5462TUJG/) 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/IGVFDS2549GCKW/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS2612LSTD/",
            "accession": "IGVFDS2612LSTD",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_sgRNA_LW281"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "preview"
        },
        {
            "@id": "/auxiliary-sets/IGVFDS2549GCKW/",
            "accession": "IGVFDS2549GCKW",
            "aliases": [
                "gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_HTO_LW281"
            ],
            "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": "2024-02-29T16:52:20.759243+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/IGVFFI6060RUDC/",
            "accession": "IGVFFI6060RUDC",
            "aliases": [
                "gary-hon:LW281_2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:18:22.632924+00:00",
            "file_format": "fastq",
            "file_size": 74905345,
            "href": "/sequence-files/IGVFFI6060RUDC/@@download/IGVFFI6060RUDC.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/c5a5525c-9429-400c-a291-878e4f2c3532/IGVFFI6060RUDC.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW281_S19_L002_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1727DJMY/",
            "accession": "IGVFFI1727DJMY",
            "aliases": [
                "gary-hon:LW281_2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:18:37.152073+00:00",
            "file_format": "fastq",
            "file_size": 503283129,
            "href": "/sequence-files/IGVFFI1727DJMY/@@download/IGVFFI1727DJMY.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/d7d49603-4bce-4435-aed2-1b4e35a72fbb/IGVFFI1727DJMY.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW281_S19_L002_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5007DWHI/",
            "accession": "IGVFFI5007DWHI",
            "aliases": [
                "gary-hon:LW281_2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:18:31.648172+00:00",
            "file_format": "fastq",
            "file_size": 215223274,
            "href": "/sequence-files/IGVFFI5007DWHI/@@download/IGVFFI5007DWHI.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/55604513-018d-4ee8-8166-2b32280bbfb2/IGVFFI5007DWHI.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW281_S19_L002_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9041LHWG/",
            "accession": "IGVFFI9041LHWG",
            "aliases": [
                "gary-hon:LW281_1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:18:14.530624+00:00",
            "file_format": "fastq",
            "file_size": 510779956,
            "href": "/sequence-files/IGVFFI9041LHWG/@@download/IGVFFI9041LHWG.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/316674a6-bc11-49c3-ba51-12ce884e0be7/IGVFFI9041LHWG.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW281_S19_L001_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7614TPCO/",
            "accession": "IGVFFI7614TPCO",
            "aliases": [
                "gary-hon:LW281_1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:18:04.418758+00:00",
            "file_format": "fastq",
            "file_size": 79079512,
            "href": "/sequence-files/IGVFFI7614TPCO/@@download/IGVFFI7614TPCO.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/57be1d3d-8040-43f0-b199-1545de15f951/IGVFFI7614TPCO.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW281_S19_L001_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6389SAKA/",
            "accession": "IGVFFI6389SAKA",
            "aliases": [
                "gary-hon:LW281_2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:18:27.113168+00:00",
            "file_format": "fastq",
            "file_size": 76312078,
            "href": "/sequence-files/IGVFFI6389SAKA/@@download/IGVFFI6389SAKA.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/d86601a8-9ffb-4d82-824b-dcca37bf56f1/IGVFFI6389SAKA.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW281_S19_L002_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6933IHKQ/",
            "accession": "IGVFFI6933IHKQ",
            "aliases": [
                "gary-hon:LW281_1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:17:59.853043+00:00",
            "file_format": "fastq",
            "file_size": 75201613,
            "href": "/sequence-files/IGVFFI6933IHKQ/@@download/IGVFFI6933IHKQ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/edab6ebd-487a-46d3-8260-71c30073ba3d/IGVFFI6933IHKQ.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW281_S19_L001_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0239MXTR/",
            "accession": "IGVFFI0239MXTR",
            "aliases": [
                "gary-hon:LW281_1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-03-01T17:18:08.868753+00:00",
            "file_format": "fastq",
            "file_size": 217365666,
            "href": "/sequence-files/IGVFFI0239MXTR/@@download/IGVFFI0239MXTR.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/03/01/d757be89-013a-436e-b9bd-733045ec5db1/IGVFFI0239MXTR.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW281_S19_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS1588TVKF/"
    ],
    "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/IGVFSM0956HKRJ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0956HKRJ",
            "aliases": [
                "nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW281"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "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) differentiated cell specimen induced to neural stem cell for 20 days (cellular sub pool: subpool_LW281), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000047/",
                "status": "preview",
                "term_name": "neural stem cell"
            },
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "23",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
        "title": "Mpathi Nzima"
    },
    "submitted_files_timestamp": "2024-03-01T17:16:17.730047+00:00",
    "submitter_comment": "Transcriptiome for LW281",
    "summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
    "uuid": "77c7030f-51f9-42c0-8c20-5c13dc904794"
}