IGVFFI8487QYZL

preview
validated
{
    "@context": "/terms/",
    "@id": "/matrix-files/IGVFFI8487QYZL/",
    "@type": [
        "MatrixFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI8487QYZL",
    "aliases": [
        "gary-hon:WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_PrimaryAnalysis_pkl"
    ],
    "analysis_step_version": "/analysis-step-versions/65c095ee-8330-48d0-bc03-d930326fe393/",
    "assay_titles": [
        "Perturb-seq"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Preview matrix file [IGVFFI8487QYZL](/matrix-files/IGVFFI8487QYZL/) has in progress subobject analysis step version [65c095ee-8330-48d0-bc03-d930326fe393](/analysis-step-versions/65c095ee-8330-48d0-bc03-d930326fe393/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/matrix-files/IGVFFI8487QYZL/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing file format specifications",
                "detail": "Matrix file [IGVFFI8487QYZL](/matrix-files/IGVFFI8487QYZL/) has no `file_format_specifications`. Matrix files are expected to link to a file format specifications document describing the axes and layers of the file.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_file_no_file_format_specifications",
                "path": "/matrix-files/IGVFFI8487QYZL/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG011996/",
        "component": "functional characterization"
    },
    "content_summary": "cell by CRISPR guide capture in raw feature barcode matrix",
    "content_type": "raw feature barcode matrix",
    "creation_timestamp": "2024-12-17T23:40:13.934021+00:00",
    "derived_from": [
        "/sequence-files/IGVFFI6060RUDC/",
        "/sequence-files/IGVFFI1727DJMY/",
        "/sequence-files/IGVFFI5007DWHI/",
        "/sequence-files/IGVFFI9041LHWG/",
        "/sequence-files/IGVFFI7614TPCO/",
        "/sequence-files/IGVFFI6389SAKA/",
        "/sequence-files/IGVFFI6933IHKQ/",
        "/sequence-files/IGVFFI0239MXTR/",
        "/sequence-files/IGVFFI6611BGPK/",
        "/sequence-files/IGVFFI4582VNCZ/",
        "/sequence-files/IGVFFI1807ZQQP/",
        "/sequence-files/IGVFFI6515ZKTF/",
        "/sequence-files/IGVFFI4919JJPZ/",
        "/sequence-files/IGVFFI8349NVKT/",
        "/sequence-files/IGVFFI5164GGZB/",
        "/sequence-files/IGVFFI4061QSKL/",
        "/sequence-files/IGVFFI4327UMKJ/",
        "/sequence-files/IGVFFI3275IUJQ/",
        "/sequence-files/IGVFFI0782ZJOJ/",
        "/sequence-files/IGVFFI0713WITI/",
        "/sequence-files/IGVFFI4515BKOL/",
        "/sequence-files/IGVFFI2642JAIF/",
        "/sequence-files/IGVFFI8312SSMA/",
        "/sequence-files/IGVFFI5462TUJG/",
        "/sequence-files/IGVFFI5962SCOE/",
        "/sequence-files/IGVFFI0480OGUQ/",
        "/sequence-files/IGVFFI0724COUK/",
        "/sequence-files/IGVFFI6944QPBK/",
        "/sequence-files/IGVFFI2488TFIW/",
        "/sequence-files/IGVFFI5032ZZGX/",
        "/sequence-files/IGVFFI6517QDFT/",
        "/sequence-files/IGVFFI9269XLGJ/",
        "/sequence-files/IGVFFI9536AHMJ/",
        "/sequence-files/IGVFFI2700GHXT/",
        "/sequence-files/IGVFFI9141KKTA/",
        "/sequence-files/IGVFFI3164PDJY/",
        "/sequence-files/IGVFFI3852EJBS/",
        "/sequence-files/IGVFFI3491WALI/",
        "/sequence-files/IGVFFI2014MVWI/",
        "/sequence-files/IGVFFI3418CTXX/",
        "/sequence-files/IGVFFI1692PBQW/",
        "/sequence-files/IGVFFI5482BVUW/",
        "/sequence-files/IGVFFI9298IPBX/",
        "/sequence-files/IGVFFI0409KOWK/",
        "/sequence-files/IGVFFI3785WYDT/",
        "/sequence-files/IGVFFI5436EVPV/",
        "/sequence-files/IGVFFI2912RLLI/",
        "/sequence-files/IGVFFI4099YBZW/",
        "/sequence-files/IGVFFI3964ARVE/",
        "/sequence-files/IGVFFI3233FBMS/",
        "/sequence-files/IGVFFI1317OLKM/",
        "/sequence-files/IGVFFI6072QDBA/",
        "/sequence-files/IGVFFI7655ZVVE/",
        "/sequence-files/IGVFFI8428EQHY/",
        "/sequence-files/IGVFFI9367DVXT/",
        "/sequence-files/IGVFFI5841BYNF/",
        "/sequence-files/IGVFFI1665CADL/",
        "/sequence-files/IGVFFI3519VNMQ/",
        "/sequence-files/IGVFFI2060GRST/",
        "/sequence-files/IGVFFI8010OOFR/",
        "/sequence-files/IGVFFI9758LRXH/",
        "/sequence-files/IGVFFI6625XXQD/",
        "/sequence-files/IGVFFI1976NIRG/",
        "/sequence-files/IGVFFI1491BIMR/",
        "/sequence-files/IGVFFI5245DMCW/",
        "/sequence-files/IGVFFI3918UPES/",
        "/sequence-files/IGVFFI7518XBAK/",
        "/sequence-files/IGVFFI9972BHWI/",
        "/sequence-files/IGVFFI8032BRVG/",
        "/sequence-files/IGVFFI6392ULTE/",
        "/sequence-files/IGVFFI2868ZCYM/",
        "/sequence-files/IGVFFI9747MXBT/",
        "/sequence-files/IGVFFI0567LHAG/",
        "/sequence-files/IGVFFI0729NJWD/",
        "/sequence-files/IGVFFI5586QFMY/",
        "/sequence-files/IGVFFI2725QQFG/",
        "/sequence-files/IGVFFI0060LELM/",
        "/sequence-files/IGVFFI9833YXEJ/",
        "/sequence-files/IGVFFI3869NPKN/",
        "/sequence-files/IGVFFI2466VXVK/",
        "/sequence-files/IGVFFI2235WFJR/",
        "/sequence-files/IGVFFI3240FCBJ/",
        "/sequence-files/IGVFFI5213ZPGN/",
        "/sequence-files/IGVFFI7051FHND/",
        "/sequence-files/IGVFFI8462WRNK/",
        "/sequence-files/IGVFFI1428MDRF/",
        "/sequence-files/IGVFFI8576TNCS/",
        "/sequence-files/IGVFFI9815IGUY/",
        "/sequence-files/IGVFFI7707CNCP/",
        "/sequence-files/IGVFFI7180TCQN/",
        "/sequence-files/IGVFFI4098UEYI/",
        "/sequence-files/IGVFFI0338ZIDU/",
        "/sequence-files/IGVFFI2183YERZ/",
        "/sequence-files/IGVFFI2451CCHU/",
        "/sequence-files/IGVFFI7688VJBW/",
        "/sequence-files/IGVFFI7643DOED/"
    ],
    "file_format": "pkl",
    "file_set": {
        "@id": "/analysis-sets/IGVFDS1588TVKF/",
        "@type": [
            "AnalysisSet",
            "FileSet",
            "Item"
        ],
        "accession": "IGVFDS1588TVKF",
        "file_set_type": "principal analysis",
        "samples": [
            {
                "@id": "/in-vitro-systems/IGVFSM1288TQKF/",
                "@type": [
                    "InVitroSystem",
                    "Biosample",
                    "Sample",
                    "Item"
                ],
                "accession": "IGVFSM1288TQKF",
                "classifications": [
                    "differentiated cell specimen"
                ],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
                        "modality": "interference",
                        "status": "preview",
                        "summary": "CRISPRi Sp-dCas9"
                    }
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0009747/",
                        "status": "released",
                        "term_name": "GM25256 (WTC-11)"
                    }
                ],
                "status": "preview",
                "summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to neural stem cell for 20 days (cellular sub pool: subpool_LW282) 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"
            },
            {
                "@id": "/in-vitro-systems/IGVFSM2597WGYB/",
                "@type": [
                    "InVitroSystem",
                    "Biosample",
                    "Sample",
                    "Item"
                ],
                "accession": "IGVFSM2597WGYB",
                "classifications": [
                    "differentiated cell specimen"
                ],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
                        "modality": "interference",
                        "status": "preview",
                        "summary": "CRISPRi Sp-dCas9"
                    }
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0009747/",
                        "status": "released",
                        "term_name": "GM25256 (WTC-11)"
                    }
                ],
                "status": "preview",
                "summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to neural stem cell for 20 days (cellular sub pool: subpool_LW284) 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"
            },
            {
                "@id": "/in-vitro-systems/IGVFSM0956HKRJ/",
                "@type": [
                    "InVitroSystem",
                    "Biosample",
                    "Sample",
                    "Item"
                ],
                "accession": "IGVFSM0956HKRJ",
                "classifications": [
                    "differentiated cell specimen"
                ],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
                        "modality": "interference",
                        "status": "preview",
                        "summary": "CRISPRi Sp-dCas9"
                    }
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0009747/",
                        "status": "released",
                        "term_name": "GM25256 (WTC-11)"
                    }
                ],
                "status": "preview",
                "summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to neural stem cell for 20 days (cellular sub pool: subpool_LW281) 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"
            },
            {
                "@id": "/in-vitro-systems/IGVFSM8464JMJS/",
                "@type": [
                    "InVitroSystem",
                    "Biosample",
                    "Sample",
                    "Item"
                ],
                "accession": "IGVFSM8464JMJS",
                "classifications": [
                    "differentiated cell specimen"
                ],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
                        "modality": "interference",
                        "status": "preview",
                        "summary": "CRISPRi Sp-dCas9"
                    }
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0009747/",
                        "status": "released",
                        "term_name": "GM25256 (WTC-11)"
                    }
                ],
                "status": "preview",
                "summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to neural stem cell for 20 days (cellular sub pool: subpool_LW283) 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"
            }
        ],
        "status": "preview",
        "summary": "interference Perturb-seq: filtered feature barcode matrix, raw feature barcode matrix, sparse gene count matrix"
    },
    "file_size": 540005995,
    "gene_list_for": [],
    "href": "/matrix-files/IGVFFI8487QYZL/@@download/IGVFFI8487QYZLpkl",
    "input_file_for": [
        "/matrix-files/IGVFFI0412HTWJ/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/gary-hon/",
        "title": "Gary Hon, UT"
    },
    "loci_list_for": [],
    "md5sum": "c4e133e8ead6bb5219dfec323bd796c1",
    "principal_dimension": "cell",
    "quality_metrics": [],
    "reference_files": [
        "/reference-files/IGVFFI6815WBWB/"
    ],
    "s3_uri": "s3://igvf-files/2024/12/17/45e4e140-eb79-4938-aeca-a0dd81528ecf/IGVFFI8487QYZLpkl",
    "schema_version": "7",
    "secondary_dimensions": [
        "CRISPR guide capture"
    ],
    "status": "preview",
    "submitted_by": {
        "@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
        "title": "Mpathi Nzima"
    },
    "submitted_file_name": "/project/GCRB/Hon_lab/s215194/Single_Cell/TF_perturb_seq/_pipeline_reporcessing/_combined_npc/aggr_dataframe/aggr_combined_df_full.pkl",
    "summary": "cell by CRISPR guide capture in raw feature barcode matrix",
    "upload_status": "validated",
    "uuid": "45e4e140-eb79-4938-aeca-a0dd81528ecf",
    "workflow": {
        "@id": "/workflows/IGVFWF0190YALU/",
        "name": "Hon Perturb-seq Workflow",
        "uniform_pipeline": false
    }
}