IGVFFI4224VTMB

released
validated
{
    "@context": "/terms/",
    "@id": "/alignment-files/IGVFFI4224VTMB/",
    "@type": [
        "AlignmentFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI4224VTMB",
    "aliases": [
        "charles-gersbach:jurkats-alignment-crispra-vp64x2-il2ra-low-bin-rep1"
    ],
    "analysis_step_version": "/analysis-step-versions/f9f6ae88-d515-4e49-9902-deea3cf87703/",
    "assay_titles": [
        "CRISPR FACS screen"
    ],
    "assembly": "custom",
    "audit": {},
    "award": {
        "@id": "/awards/HG012053/",
        "component": "functional characterization"
    },
    "content_md5sum": "28b5a4733cf0ad52fd3784a2d01ca610",
    "content_summary": "unfiltered alignments",
    "content_type": "alignments",
    "controlled_access": false,
    "creation_timestamp": "2024-10-15T19:05:54.491083+00:00",
    "derived_from": [
        "/sequence-files/IGVFFI6670AAFN/"
    ],
    "file_format": "bam",
    "file_set": {
        "@id": "/analysis-sets/IGVFDS5218AVPW/",
        "accession": "IGVFDS5218AVPW",
        "file_set_type": "intermediate analysis",
        "samples": [
            {
                "@id": "/in-vitro-systems/IGVFSM1838CFFU/",
                "accession": "IGVFSM1838CFFU",
                "classifications": [
                    "cell line"
                ],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/4c532ce1-11aa-41be-9757-13923c19248b/",
                        "modality": "activation",
                        "summary": "CRISPRa Sa-dCas9-2xVP64"
                    }
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0002796/",
                        "term_name": "Jurkat"
                    }
                ],
                "summary": "Jurkat cell line, Homo sapiens (sorting details: FACS bin for 0-10% expression of IL2RA ) modified with CRISPRa Sa-dCas9-2xVP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            },
            {
                "@id": "/in-vitro-systems/IGVFSM2429HKWG/",
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                        "@id": "/crispr-modifications/4c532ce1-11aa-41be-9757-13923c19248b/",
                        "modality": "activation",
                        "summary": "CRISPRa Sa-dCas9-2xVP64"
                    }
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0002796/",
                        "term_name": "Jurkat"
                    }
                ],
                "summary": "Jurkat cell line, Homo sapiens (sorting details: FACS bin for 0-10% expression of IL2RA ) modified with CRISPRa Sa-dCas9-2xVP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            },
            {
                "@id": "/in-vitro-systems/IGVFSM4817IZZH/",
                "accession": "IGVFSM4817IZZH",
                "classifications": [
                    "cell line"
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                "modifications": [
                    {
                        "@id": "/crispr-modifications/4c532ce1-11aa-41be-9757-13923c19248b/",
                        "modality": "activation",
                        "summary": "CRISPRa Sa-dCas9-2xVP64"
                    }
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0002796/",
                        "term_name": "Jurkat"
                    }
                ],
                "summary": "Jurkat cell line, Homo sapiens (sorting details: FACS bin for 90-100% expression of IL2RA ) modified with CRISPRa Sa-dCas9-2xVP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            },
            {
                "@id": "/in-vitro-systems/IGVFSM6964ODEE/",
                "accession": "IGVFSM6964ODEE",
                "classifications": [
                    "cell line"
                ],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/4c532ce1-11aa-41be-9757-13923c19248b/",
                        "modality": "activation",
                        "summary": "CRISPRa Sa-dCas9-2xVP64"
                    }
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0002796/",
                        "term_name": "Jurkat"
                    }
                ],
                "summary": "Jurkat cell line, Homo sapiens (sorting details: FACS bin for 90-100% expression of IL2RA ) modified with CRISPRa Sa-dCas9-2xVP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            },
            {
                "@id": "/in-vitro-systems/IGVFSM3244YHOI/",
                "accession": "IGVFSM3244YHOI",
                "classifications": [
                    "cell line"
                ],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/4c532ce1-11aa-41be-9757-13923c19248b/",
                        "modality": "activation",
                        "summary": "CRISPRa Sa-dCas9-2xVP64"
                    }
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0002796/",
                        "term_name": "Jurkat"
                    }
                ],
                "summary": "Jurkat cell line, Homo sapiens (sorting details: FACS bin for 90-100% expression of IL2RA ) modified with CRISPRa Sa-dCas9-2xVP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            },
            {
                "@id": "/in-vitro-systems/IGVFSM5112IFQB/",
                "accession": "IGVFSM5112IFQB",
                "classifications": [
                    "cell line"
                ],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/4c532ce1-11aa-41be-9757-13923c19248b/",
                        "modality": "activation",
                        "summary": "CRISPRa Sa-dCas9-2xVP64"
                    }
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0002796/",
                        "term_name": "Jurkat"
                    }
                ],
                "summary": "Jurkat cell line, Homo sapiens (sorting details: FACS bin for 0-10% expression of IL2RA ) modified with CRISPRa Sa-dCas9-2xVP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            }
        ],
        "summary": "CRISPR activation FACS screen targeting IL2RA: alignments"
    },
    "file_size": 17342607,
    "filtered": false,
    "gene_list_for": [],
    "href": "/alignment-files/IGVFFI4224VTMB/@@download/IGVFFI4224VTMB.bam",
    "input_file_for": [
        "/tabular-files/IGVFFI4074JRJB/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "loci_list_for": [],
    "md5sum": "4c8eb607f2eb92ec82448f1f75cc9a57",
    "read_count": 1166714,
    "redacted": false,
    "reference_files": [
        "/reference-files/IGVFFI5804OZJN/"
    ],
    "release_timestamp": "2024-11-18T21:08:59.517468+00:00",
    "s3_uri": "s3://igvf-files/2024/10/15/22ed2231-fef7-4487-80d8-d88519029790/IGVFFI4224VTMB.bam",
    "schema_version": "11",
    "status": "released",
    "submitted_by": {
        "@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
        "title": "Alejandro Barrera"
    },
    "submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/pSM26-Low-R1_S1.sorted.bam",
    "summary": "custom assembly unfiltered alignments",
    "upload_status": "validated",
    "uuid": "22ed2231-fef7-4487-80d8-d88519029790"
}