IGVFDS0120YHME

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS0120YHME/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS0120YHME",
    "aliases": [
        "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA_AmpliconSequencing"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003133/",
        "term_name": "cas mediated mutagenesis"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released in vitro system [IGVFSM4133KDLM](/in-vitro-systems/IGVFSM4133KDLM/) has in progress subobject construct library set [IGVFDS6377KNCH](/construct-library-sets/IGVFDS6377KNCH/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/in-vitro-systems/IGVFSM4133KDLM/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS0120YHME](/measurement-sets/IGVFDS0120YHME/) has sequence file(s): [IGVFFI8471SQCM](/sequence-files/IGVFFI8471SQCM/), [IGVFFI2987HUNV](/sequence-files/IGVFFI2987HUNV/), [IGVFFI1659GJXT](/sequence-files/IGVFFI1659GJXT/), [IGVFFI8572LIGU](/sequence-files/IGVFFI8572LIGU/), [IGVFFI1487ILZL](/sequence-files/IGVFFI1487ILZL/), [IGVFFI0523CAKB](/sequence-files/IGVFFI0523CAKB/), [IGVFFI0174SRME](/sequence-files/IGVFFI0174SRME/), [IGVFFI0536RYTX](/sequence-files/IGVFFI0536RYTX/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_missing_seqspec",
                "path": "/measurement-sets/IGVFDS0120YHME/"
            },
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS0120YHME](/measurement-sets/IGVFDS0120YHME/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_CRISPR_assay_missing_cell_sorting_auxiliary_set",
                "path": "/measurement-sets/IGVFDS0120YHME/"
            },
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS0120YHME](/measurement-sets/IGVFDS0120YHME/) has no variant sequencing `auxiliary_sets`. Variant FlowFISH measurement sets are expected to link to a variant sequencing auxiliary set.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_Variant_FlowFISH_missing_variant_sequencing_auxiliary_set",
                "path": "/measurement-sets/IGVFDS0120YHME/"
            }
        ],
        "WARNING": [
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS0120YHME](/measurement-sets/IGVFDS0120YHME/) has sequence file(s) [IGVFFI8471SQCM](/sequence-files/IGVFFI8471SQCM/), [IGVFFI2987HUNV](/sequence-files/IGVFFI2987HUNV/), [IGVFFI1659GJXT](/sequence-files/IGVFFI1659GJXT/), [IGVFFI8572LIGU](/sequence-files/IGVFFI8572LIGU/), [IGVFFI1487ILZL](/sequence-files/IGVFFI1487ILZL/), [IGVFFI0523CAKB](/sequence-files/IGVFFI0523CAKB/), [IGVFFI0174SRME](/sequence-files/IGVFFI0174SRME/), [IGVFFI0536RYTX](/sequence-files/IGVFFI0536RYTX/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/measurement-sets/IGVFDS0120YHME/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG011972/",
        "component": "functional characterization",
        "contact_pi": {
            "@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
            "title": "Jesse Engreitz"
        },
        "title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
    },
    "control_file_sets": [
        {
            "@id": "/measurement-sets/IGVFDS9477ARWI/",
            "accession": "IGVFDS9477ARWI",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing",
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing"
            ]
        }
    ],
    "control_for": [],
    "creation_timestamp": "2023-11-30T22:47:14.893103+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1080XFGV/",
            "accession": "IGVFDO1080XFGV",
            "aliases": [
                "igvf:donor_of_Jurkat"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI8471SQCM/",
            "accession": "IGVFFI8471SQCM",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep1_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T18:41:56.611093+00:00",
            "file_format": "fastq",
            "file_size": 7699605,
            "href": "/sequence-files/IGVFFI8471SQCM/@@download/IGVFFI8471SQCM.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/1cd70039-f69e-468e-8552-d510efd3a042/IGVFFI8471SQCM.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "term_name": "Illumina NextSeq 550"
            },
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S5-BioRep2-FFRep1-BinA-PCRrep1_S15_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2987HUNV/",
            "accession": "IGVFFI2987HUNV",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep2_R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T18:48:14.994003+00:00",
            "file_format": "fastq",
            "file_size": 7856990,
            "href": "/sequence-files/IGVFFI2987HUNV/@@download/IGVFFI2987HUNV.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/a2e9fd82-d84a-4a71-8ef7-ee904d0dc0ca/IGVFFI2987HUNV.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "term_name": "Illumina NextSeq 550"
            },
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S5-BioRep2-FFRep1-BinA-PCRrep2_S71_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1659GJXT/",
            "accession": "IGVFFI1659GJXT",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep1_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T18:54:38.094124+00:00",
            "file_format": "fastq",
            "file_size": 13949069,
            "href": "/sequence-files/IGVFFI1659GJXT/@@download/IGVFFI1659GJXT.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/13dac7fd-772c-4573-8b70-cd6349c2b08d/IGVFFI1659GJXT.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "term_name": "Illumina NextSeq 550"
            },
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S5-BioRep2-FFRep1-BinA-PCRrep1_S15_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8572LIGU/",
            "accession": "IGVFFI8572LIGU",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep2_R2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:01:15.566185+00:00",
            "file_format": "fastq",
            "file_size": 14281631,
            "href": "/sequence-files/IGVFFI8572LIGU/@@download/IGVFFI8572LIGU.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/a8063324-a50d-4eba-85a6-902d6c0e101f/IGVFFI8572LIGU.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "term_name": "Illumina NextSeq 550"
            },
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S5-BioRep2-FFRep1-BinA-PCRrep2_S71_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1487ILZL/",
            "accession": "IGVFFI1487ILZL",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep1_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:07:40.963677+00:00",
            "file_format": "fastq",
            "file_size": 3142539,
            "href": "/sequence-files/IGVFFI1487ILZL/@@download/IGVFFI1487ILZL.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/1f196ef8-0721-46b3-b4bb-5e5168944749/IGVFFI1487ILZL.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "term_name": "Illumina NextSeq 550"
            },
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S5-BioRep2-FFRep1-BinA-PCRrep1_S15_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0523CAKB/",
            "accession": "IGVFFI0523CAKB",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep2_I1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:13:55.779178+00:00",
            "file_format": "fastq",
            "file_size": 3334248,
            "href": "/sequence-files/IGVFFI0523CAKB/@@download/IGVFFI0523CAKB.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/483169f2-ce0e-4712-ae4b-ffca0e69ef23/IGVFFI0523CAKB.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "term_name": "Illumina NextSeq 550"
            },
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S5-BioRep2-FFRep1-BinA-PCRrep2_S71_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0174SRME/",
            "accession": "IGVFFI0174SRME",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep1_I2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:20:11.230864+00:00",
            "file_format": "fastq",
            "file_size": 3116176,
            "href": "/sequence-files/IGVFFI0174SRME/@@download/IGVFFI0174SRME.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/9539f913-88b7-44c9-ba8a-9fd4242c5938/IGVFFI0174SRME.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "term_name": "Illumina NextSeq 550"
            },
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S5-BioRep2-FFRep1-BinA-PCRrep1_S15_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0536RYTX/",
            "accession": "IGVFFI0536RYTX",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep2_I2"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-12-05T19:26:31.898855+00:00",
            "file_format": "fastq",
            "file_size": 3166111,
            "href": "/sequence-files/IGVFFI0536RYTX/@@download/IGVFFI0536RYTX.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/5e30bf92-c926-4f98-88f1-ec7b7e82a95b/IGVFFI0536RYTX.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "term_name": "Illumina NextSeq 550"
            },
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S5-BioRep2-FFRep1-BinA-PCRrep2_S71_I2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_file_set_for": [
        "/analysis-sets/IGVFDS9162RHFP/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
    "preferred_assay_title": "Variant FlowFISH",
    "protocols": [
        "https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
    ],
    "release_timestamp": "2023-12-20T23:03:39.125133+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM4133KDLM/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4133KDLM",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS6377KNCH/",
                    "accession": "IGVFDS6377KNCH",
                    "file_set_type": "guide library",
                    "summary": "Guide (sgRNA) library targeting sequence variants in a genomic locus"
                }
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
                    "modality": "prime editing"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002796/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:Jurkat"
                    ],
                    "status": "released",
                    "summary": "Jurkat",
                    "term_name": "Jurkat"
                }
            ],
            "status": "released",
            "summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 0-10% expression of PPIF) modified with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "17",
    "status": "released",
    "submitted_by": {
        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
        "title": "Michael Montgomery"
    },
    "submitted_files_timestamp": "2023-12-05T18:41:56.611093+00:00",
    "summary": "cas mediated mutagenesis (Variant FlowFISH) integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
    "uuid": "cca32d78-ea12-41cd-9ba1-0e3886feca00"
}