{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9252NUTS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9252NUTS",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9252NUTS](/measurement-sets/IGVFDS9252NUTS/) has sequence file(s) [IGVFFI6822HPEI](/sequence-files/IGVFFI6822HPEI/), [IGVFFI1071XPSL](/sequence-files/IGVFFI1071XPSL/), [IGVFFI0748SFGU](/sequence-files/IGVFFI0748SFGU/), [IGVFFI9626WVUX](/sequence-files/IGVFFI9626WVUX/), [IGVFFI3315DJBA](/sequence-files/IGVFFI3315DJBA/), [IGVFFI2662PDNZ](/sequence-files/IGVFFI2662PDNZ/), [IGVFFI7293QPPK](/sequence-files/IGVFFI7293QPPK/), [IGVFFI6522YJLY](/sequence-files/IGVFFI6522YJLY/), [IGVFFI1894UCED](/sequence-files/IGVFFI1894UCED/), [IGVFFI9404RZGR](/sequence-files/IGVFFI9404RZGR/), [IGVFFI7799MQIM](/sequence-files/IGVFFI7799MQIM/), [IGVFFI9278LCWP](/sequence-files/IGVFFI9278LCWP/), [IGVFFI4538ZCMP](/sequence-files/IGVFFI4538ZCMP/), [IGVFFI7461RCIG](/sequence-files/IGVFFI7461RCIG/), [IGVFFI2792GDJT](/sequence-files/IGVFFI2792GDJT/), [IGVFFI2201UKQJ](/sequence-files/IGVFFI2201UKQJ/), [IGVFFI9165UXXA](/sequence-files/IGVFFI9165UXXA/), [IGVFFI3278PORX](/sequence-files/IGVFFI3278PORX/), [IGVFFI3836LQAS](/sequence-files/IGVFFI3836LQAS/), [IGVFFI4142LJAS](/sequence-files/IGVFFI4142LJAS/), [IGVFFI4416VUJB](/sequence-files/IGVFFI4416VUJB/), [IGVFFI7096WYEQ](/sequence-files/IGVFFI7096WYEQ/), [IGVFFI2762XZJN](/sequence-files/IGVFFI2762XZJN/), [IGVFFI9246ZKTD](/sequence-files/IGVFFI9246ZKTD/), [IGVFFI9376YQFI](/sequence-files/IGVFFI9376YQFI/), [IGVFFI2649LOBN](/sequence-files/IGVFFI2649LOBN/), [IGVFFI7838ZOSV](/sequence-files/IGVFFI7838ZOSV/), [IGVFFI2858NGQX](/sequence-files/IGVFFI2858NGQX/), [IGVFFI9264LJHM](/sequence-files/IGVFFI9264LJHM/), [IGVFFI9100EKLU](/sequence-files/IGVFFI9100EKLU/), [IGVFFI3747WKJN](/sequence-files/IGVFFI3747WKJN/), [IGVFFI7906VNKW](/sequence-files/IGVFFI7906VNKW/) 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/IGVFDS9252NUTS/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9252NUTS](/measurement-sets/IGVFDS9252NUTS/) has sequence file(s): [IGVFFI6822HPEI](/sequence-files/IGVFFI6822HPEI/), [IGVFFI1071XPSL](/sequence-files/IGVFFI1071XPSL/), [IGVFFI0748SFGU](/sequence-files/IGVFFI0748SFGU/), [IGVFFI9626WVUX](/sequence-files/IGVFFI9626WVUX/), [IGVFFI3315DJBA](/sequence-files/IGVFFI3315DJBA/), [IGVFFI2662PDNZ](/sequence-files/IGVFFI2662PDNZ/), [IGVFFI7293QPPK](/sequence-files/IGVFFI7293QPPK/), [IGVFFI6522YJLY](/sequence-files/IGVFFI6522YJLY/), [IGVFFI1894UCED](/sequence-files/IGVFFI1894UCED/), [IGVFFI9404RZGR](/sequence-files/IGVFFI9404RZGR/), [IGVFFI7799MQIM](/sequence-files/IGVFFI7799MQIM/), [IGVFFI9278LCWP](/sequence-files/IGVFFI9278LCWP/), [IGVFFI4538ZCMP](/sequence-files/IGVFFI4538ZCMP/), [IGVFFI7461RCIG](/sequence-files/IGVFFI7461RCIG/), [IGVFFI2792GDJT](/sequence-files/IGVFFI2792GDJT/), [IGVFFI2201UKQJ](/sequence-files/IGVFFI2201UKQJ/), [IGVFFI9165UXXA](/sequence-files/IGVFFI9165UXXA/), [IGVFFI3278PORX](/sequence-files/IGVFFI3278PORX/), [IGVFFI3836LQAS](/sequence-files/IGVFFI3836LQAS/), [IGVFFI4142LJAS](/sequence-files/IGVFFI4142LJAS/), [IGVFFI4416VUJB](/sequence-files/IGVFFI4416VUJB/), [IGVFFI7096WYEQ](/sequence-files/IGVFFI7096WYEQ/), [IGVFFI2762XZJN](/sequence-files/IGVFFI2762XZJN/), [IGVFFI9246ZKTD](/sequence-files/IGVFFI9246ZKTD/), [IGVFFI9376YQFI](/sequence-files/IGVFFI9376YQFI/), [IGVFFI2649LOBN](/sequence-files/IGVFFI2649LOBN/), [IGVFFI7838ZOSV](/sequence-files/IGVFFI7838ZOSV/), [IGVFFI2858NGQX](/sequence-files/IGVFFI2858NGQX/), [IGVFFI9264LJHM](/sequence-files/IGVFFI9264LJHM/), [IGVFFI9100EKLU](/sequence-files/IGVFFI9100EKLU/), [IGVFFI3747WKJN](/sequence-files/IGVFFI3747WKJN/), [IGVFFI7906VNKW](/sequence-files/IGVFFI7906VNKW/) 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/IGVFDS9252NUTS/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM8750WCGQ](/in-vitro-systems/IGVFSM8750WCGQ/) has in progress subobject treatment [cf87f410-54ee-48ef-b654-8443c4fee032](/treatments/cf87f410-54ee-48ef-b654-8443c4fee032/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM8750WCGQ/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM8750WCGQ](/in-vitro-systems/IGVFSM8750WCGQ/) has in progress subobject treatment [4b5f0d13-ec20-4b91-85f5-a009cd91451f](/treatments/4b5f0d13-ec20-4b91-85f5-a009cd91451f/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM8750WCGQ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9252NUTS](/measurement-sets/IGVFDS9252NUTS/) 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": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS9252NUTS/"
}
]
},
"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/IGVFDS6874YIXA/",
"accession": "IGVFDS6874YIXA",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-22T00:47:39.581538+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI6822HPEI/",
"accession": "IGVFFI6822HPEI",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T06:04:41.668420+00:00",
"file_format": "fastq",
"file_size": 5727492,
"href": "/sequence-files/IGVFFI6822HPEI/@@download/IGVFFI6822HPEI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/d8e5f120-adef-48d2-aada-7019bd6b56fe/IGVFFI6822HPEI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep2-BinA_S33_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1071XPSL/",
"accession": "IGVFFI1071XPSL",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T06:06:41.941498+00:00",
"file_format": "fastq",
"file_size": 11957354,
"href": "/sequence-files/IGVFFI1071XPSL/@@download/IGVFFI1071XPSL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/dcf86f2f-1a03-4c13-b0cd-f316246e2c1d/IGVFFI1071XPSL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep3-BinA_S57_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0748SFGU/",
"accession": "IGVFFI0748SFGU",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T06:08:29.615601+00:00",
"file_format": "fastq",
"file_size": 5989166,
"href": "/sequence-files/IGVFFI0748SFGU/@@download/IGVFFI0748SFGU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/8d98c046-372c-426c-a8ec-a4f31f62b0dd/IGVFFI0748SFGU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep4-BinA_S81_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9626WVUX/",
"accession": "IGVFFI9626WVUX",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T06:12:40.846648+00:00",
"file_format": "fastq",
"file_size": 6769754,
"href": "/sequence-files/IGVFFI9626WVUX/@@download/IGVFFI9626WVUX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/019cfc97-7299-4157-bfa6-09afd6aafc34/IGVFFI9626WVUX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep6-BinA_S129_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3315DJBA/",
"accession": "IGVFFI3315DJBA",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T06:02:44.064293+00:00",
"file_format": "fastq",
"file_size": 5661604,
"href": "/sequence-files/IGVFFI3315DJBA/@@download/IGVFFI3315DJBA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/dc57a1e9-124a-448c-baa3-6c4d6ac138f8/IGVFFI3315DJBA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep1-BinA_S9_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2662PDNZ/",
"accession": "IGVFFI2662PDNZ",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep5_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T06:10:31.879320+00:00",
"file_format": "fastq",
"file_size": 6666242,
"href": "/sequence-files/IGVFFI2662PDNZ/@@download/IGVFFI2662PDNZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/278d2c87-4b7b-4cdc-83f0-349edad74d16/IGVFFI2662PDNZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep5-BinA_S105_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7293QPPK/",
"accession": "IGVFFI7293QPPK",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep7_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T06:14:30.637192+00:00",
"file_format": "fastq",
"file_size": 6441700,
"href": "/sequence-files/IGVFFI7293QPPK/@@download/IGVFFI7293QPPK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/5352a34e-b50e-4f7e-b993-5688b50e832d/IGVFFI7293QPPK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep7-BinA_S153_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6522YJLY/",
"accession": "IGVFFI6522YJLY",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep8_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T06:16:24.649249+00:00",
"file_format": "fastq",
"file_size": 6735754,
"href": "/sequence-files/IGVFFI6522YJLY/@@download/IGVFFI6522YJLY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/0ba1d6e0-b5a2-4e18-972d-9752b506b244/IGVFFI6522YJLY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep8-BinA_S177_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1894UCED/",
"accession": "IGVFFI1894UCED",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep7_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:49:46.327938+00:00",
"file_format": "fastq",
"file_size": 8579730,
"href": "/sequence-files/IGVFFI1894UCED/@@download/IGVFFI1894UCED.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/b1129e2b-3d84-4711-8c0a-b39516fd139e/IGVFFI1894UCED.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep7-BinA_S153_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9404RZGR/",
"accession": "IGVFFI9404RZGR",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:50:58.635850+00:00",
"file_format": "fastq",
"file_size": 9005740,
"href": "/sequence-files/IGVFFI9404RZGR/@@download/IGVFFI9404RZGR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/c52e07d2-c526-4869-8b7d-c54f841ebce1/IGVFFI9404RZGR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep8-BinA_S177_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7799MQIM/",
"accession": "IGVFFI7799MQIM",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep5_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:47:17.566292+00:00",
"file_format": "fastq",
"file_size": 8888317,
"href": "/sequence-files/IGVFFI7799MQIM/@@download/IGVFFI7799MQIM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/0a0bbfcd-7196-4a7f-b557-f0bee7d25615/IGVFFI7799MQIM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep5-BinA_S105_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9278LCWP/",
"accession": "IGVFFI9278LCWP",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:43:26.058368+00:00",
"file_format": "fastq",
"file_size": 6240430,
"href": "/sequence-files/IGVFFI9278LCWP/@@download/IGVFFI9278LCWP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/478769c8-f9be-423c-86e7-c6bc873073dd/IGVFFI9278LCWP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep2-BinA_S33_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4538ZCMP/",
"accession": "IGVFFI4538ZCMP",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:44:48.772751+00:00",
"file_format": "fastq",
"file_size": 12895514,
"href": "/sequence-files/IGVFFI4538ZCMP/@@download/IGVFFI4538ZCMP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/5094c975-53c4-4298-8379-67b4a2e1ecba/IGVFFI4538ZCMP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep3-BinA_S57_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7461RCIG/",
"accession": "IGVFFI7461RCIG",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:46:04.211829+00:00",
"file_format": "fastq",
"file_size": 6476448,
"href": "/sequence-files/IGVFFI7461RCIG/@@download/IGVFFI7461RCIG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/6bd6644c-2317-420c-a931-b0ba309ada3a/IGVFFI7461RCIG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep4-BinA_S81_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2792GDJT/",
"accession": "IGVFFI2792GDJT",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:48:32.158868+00:00",
"file_format": "fastq",
"file_size": 9074337,
"href": "/sequence-files/IGVFFI2792GDJT/@@download/IGVFFI2792GDJT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/c06d16b2-28a4-4ca9-b4d4-f4902b33c352/IGVFFI2792GDJT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep6-BinA_S129_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2201UKQJ/",
"accession": "IGVFFI2201UKQJ",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:42:04.605838+00:00",
"file_format": "fastq",
"file_size": 6150226,
"href": "/sequence-files/IGVFFI2201UKQJ/@@download/IGVFFI2201UKQJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/bd868edc-830b-4154-8e11-cbfd1734c285/IGVFFI2201UKQJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep1-BinA_S9_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9165UXXA/",
"accession": "IGVFFI9165UXXA",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:47:22.504043+00:00",
"file_format": "fastq",
"file_size": 1630697,
"href": "/sequence-files/IGVFFI9165UXXA/@@download/IGVFFI9165UXXA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/a47d704c-e953-4bf3-9609-ff3e21d8f145/IGVFFI9165UXXA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep4-BinA_S81_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3278PORX/",
"accession": "IGVFFI3278PORX",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep8_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:52:11.224004+00:00",
"file_format": "fastq",
"file_size": 2234586,
"href": "/sequence-files/IGVFFI3278PORX/@@download/IGVFFI3278PORX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/3aa4905a-d630-465c-a5b2-1618c553166c/IGVFFI3278PORX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep8-BinA_S177_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3836LQAS/",
"accession": "IGVFFI3836LQAS",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep7_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:50:57.959535+00:00",
"file_format": "fastq",
"file_size": 2149743,
"href": "/sequence-files/IGVFFI3836LQAS/@@download/IGVFFI3836LQAS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/a6456f3a-ffdf-4936-8649-fbf562973e31/IGVFFI3836LQAS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep7-BinA_S153_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4142LJAS/",
"accession": "IGVFFI4142LJAS",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep6_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:49:47.043277+00:00",
"file_format": "fastq",
"file_size": 2285559,
"href": "/sequence-files/IGVFFI4142LJAS/@@download/IGVFFI4142LJAS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/94cdc43f-c28b-4253-b1fd-7348678265ee/IGVFFI4142LJAS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep6-BinA_S129_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4416VUJB/",
"accession": "IGVFFI4416VUJB",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:45:01.291559+00:00",
"file_format": "fastq",
"file_size": 1575562,
"href": "/sequence-files/IGVFFI4416VUJB/@@download/IGVFFI4416VUJB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/8985e11a-3969-4e12-a94a-b01c99234353/IGVFFI4416VUJB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep2-BinA_S33_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7096WYEQ/",
"accession": "IGVFFI7096WYEQ",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:46:12.839051+00:00",
"file_format": "fastq",
"file_size": 3440937,
"href": "/sequence-files/IGVFFI7096WYEQ/@@download/IGVFFI7096WYEQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/2ebf0752-8fb8-4e99-abc1-b0e10e424243/IGVFFI7096WYEQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep3-BinA_S57_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2762XZJN/",
"accession": "IGVFFI2762XZJN",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep5_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:48:34.320433+00:00",
"file_format": "fastq",
"file_size": 2136514,
"href": "/sequence-files/IGVFFI2762XZJN/@@download/IGVFFI2762XZJN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/9a0a22e1-680f-4064-88ea-36995e4aa48f/IGVFFI2762XZJN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep5-BinA_S105_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9246ZKTD/",
"accession": "IGVFFI9246ZKTD",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:43:50.150670+00:00",
"file_format": "fastq",
"file_size": 1610743,
"href": "/sequence-files/IGVFFI9246ZKTD/@@download/IGVFFI9246ZKTD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/fab04d60-7eb1-4f21-8f49-1eeb446326d3/IGVFFI9246ZKTD.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep1-BinA_S9_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9376YQFI/",
"accession": "IGVFFI9376YQFI",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep6_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:52:35.901225+00:00",
"file_format": "fastq",
"file_size": 1942865,
"href": "/sequence-files/IGVFFI9376YQFI/@@download/IGVFFI9376YQFI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/c7766fdf-7ff9-4016-a0ef-85f175287ecc/IGVFFI9376YQFI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep6-BinA_S129_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2649LOBN/",
"accession": "IGVFFI2649LOBN",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:47:20.848464+00:00",
"file_format": "fastq",
"file_size": 1536610,
"href": "/sequence-files/IGVFFI2649LOBN/@@download/IGVFFI2649LOBN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/7e25970b-d07a-41f4-a4dc-b64f04ccc8a3/IGVFFI2649LOBN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep2-BinA_S33_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7838ZOSV/",
"accession": "IGVFFI7838ZOSV",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep3_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:48:36.896201+00:00",
"file_format": "fastq",
"file_size": 3140000,
"href": "/sequence-files/IGVFFI7838ZOSV/@@download/IGVFFI7838ZOSV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/89450319-1893-4b38-8fe0-7228a9a3ef15/IGVFFI7838ZOSV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep3-BinA_S57_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2858NGQX/",
"accession": "IGVFFI2858NGQX",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:46:06.975099+00:00",
"file_format": "fastq",
"file_size": 1529937,
"href": "/sequence-files/IGVFFI2858NGQX/@@download/IGVFFI2858NGQX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/dbc9a0a2-a97d-4620-bab6-efb317cb1122/IGVFFI2858NGQX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep1-BinA_S9_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9264LJHM/",
"accession": "IGVFFI9264LJHM",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:49:54.448750+00:00",
"file_format": "fastq",
"file_size": 1608324,
"href": "/sequence-files/IGVFFI9264LJHM/@@download/IGVFFI9264LJHM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/ce2d0171-08d9-4825-80cc-632b416b60ae/IGVFFI9264LJHM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep4-BinA_S81_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9100EKLU/",
"accession": "IGVFFI9100EKLU",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep5_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:51:13.589666+00:00",
"file_format": "fastq",
"file_size": 1895967,
"href": "/sequence-files/IGVFFI9100EKLU/@@download/IGVFFI9100EKLU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/ccb145fc-b96e-44e4-8c23-53c8387d94da/IGVFFI9100EKLU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep5-BinA_S105_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3747WKJN/",
"accession": "IGVFFI3747WKJN",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep7_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:54:00.425316+00:00",
"file_format": "fastq",
"file_size": 1838521,
"href": "/sequence-files/IGVFFI3747WKJN/@@download/IGVFFI3747WKJN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/a132fba1-92fd-4cf6-b670-311a3761b0f9/IGVFFI3747WKJN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep7-BinA_S153_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7906VNKW/",
"accession": "IGVFFI7906VNKW",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA-PCRRep8_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:55:34.945949+00:00",
"file_format": "fastq",
"file_size": 1933267,
"href": "/sequence-files/IGVFFI7906VNKW/@@download/IGVFFI7906VNKW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/c728f0df-881a-4e43-bcfa-d9eaf1da4d39/IGVFFI7906VNKW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep8-BinA_S177_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1824XDMU/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "This measurement set previously used Variant FlowFISH as a preferred_assay_title, but this enum is now removed. So it has been defaulted to Variant-EFFECTS.",
"preferred_assay_title": "Variant-EFFECTS",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8750WCGQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8750WCGQ",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinA"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6128KVUP/",
"accession": "IGVFDS6128KVUP",
"file_set_type": "guide library",
"status": "preview",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
}
],
"status": "preview",
"summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 0-25% expression of IL2RA) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 24 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 24 hours, modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/4b5f0d13-ec20-4b91-85f5-a009cd91451f/",
"status": "in progress",
"treatment_term_name": "phorbol 13-acetate 12-myristate"
},
{
"@id": "/treatments/cf87f410-54ee-48ef-b654-8443c4fee032/",
"status": "in progress",
"treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain"
}
]
}
],
"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-11-22T06:02:44.064293+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000134460/",
"geneid": "ENSG00000134460",
"name": "interleukin 2 receptor subunit alpha",
"status": "released",
"symbol": "IL2RA",
"synonyms": [
"interleukin-2 receptor subunit alpha",
"IL2R",
"TAC antigen",
"IMD41",
"IL-2R subunit alpha",
"CD25",
"IL-2 receptor subunit alpha",
"IDDM10",
"TCGFR",
"p55",
"interleukin 2 receptor, alpha"
]
}
],
"uuid": "61ed9671-434f-4738-83e8-6eb86f63115d"
}