{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7995HXFV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7995HXFV",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC_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 [IGVFDS7995HXFV](/measurement-sets/IGVFDS7995HXFV/) has sequence file(s) [IGVFFI0221UHWF](/sequence-files/IGVFFI0221UHWF/), [IGVFFI8900RECT](/sequence-files/IGVFFI8900RECT/), [IGVFFI8548DYGM](/sequence-files/IGVFFI8548DYGM/), [IGVFFI0579QCYU](/sequence-files/IGVFFI0579QCYU/), [IGVFFI5769CDIM](/sequence-files/IGVFFI5769CDIM/), [IGVFFI7256NAKF](/sequence-files/IGVFFI7256NAKF/), [IGVFFI4700RBZU](/sequence-files/IGVFFI4700RBZU/), [IGVFFI9108JKFO](/sequence-files/IGVFFI9108JKFO/), [IGVFFI0101BUVS](/sequence-files/IGVFFI0101BUVS/), [IGVFFI2622TDFJ](/sequence-files/IGVFFI2622TDFJ/), [IGVFFI6897GKYL](/sequence-files/IGVFFI6897GKYL/), [IGVFFI5972PKDV](/sequence-files/IGVFFI5972PKDV/), [IGVFFI7762IALH](/sequence-files/IGVFFI7762IALH/), [IGVFFI3470ZROK](/sequence-files/IGVFFI3470ZROK/), [IGVFFI5954CAPT](/sequence-files/IGVFFI5954CAPT/), [IGVFFI0432GPRT](/sequence-files/IGVFFI0432GPRT/), [IGVFFI0067YXAS](/sequence-files/IGVFFI0067YXAS/), [IGVFFI2430FYVT](/sequence-files/IGVFFI2430FYVT/), [IGVFFI1429UHQV](/sequence-files/IGVFFI1429UHQV/), [IGVFFI8125BGTH](/sequence-files/IGVFFI8125BGTH/), [IGVFFI1975ZDMS](/sequence-files/IGVFFI1975ZDMS/), [IGVFFI9728SQIV](/sequence-files/IGVFFI9728SQIV/), [IGVFFI1495ULOM](/sequence-files/IGVFFI1495ULOM/), [IGVFFI1675XTZN](/sequence-files/IGVFFI1675XTZN/), [IGVFFI7440EWXZ](/sequence-files/IGVFFI7440EWXZ/), [IGVFFI5966TSUV](/sequence-files/IGVFFI5966TSUV/), [IGVFFI2754EDGI](/sequence-files/IGVFFI2754EDGI/), [IGVFFI9006OHQQ](/sequence-files/IGVFFI9006OHQQ/), [IGVFFI9890VGIB](/sequence-files/IGVFFI9890VGIB/), [IGVFFI8415WVOE](/sequence-files/IGVFFI8415WVOE/), [IGVFFI6984IMKC](/sequence-files/IGVFFI6984IMKC/), [IGVFFI4419NXZS](/sequence-files/IGVFFI4419NXZS/) 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/IGVFDS7995HXFV/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7995HXFV](/measurement-sets/IGVFDS7995HXFV/) has sequence file(s): [IGVFFI0221UHWF](/sequence-files/IGVFFI0221UHWF/), [IGVFFI8900RECT](/sequence-files/IGVFFI8900RECT/), [IGVFFI8548DYGM](/sequence-files/IGVFFI8548DYGM/), [IGVFFI0579QCYU](/sequence-files/IGVFFI0579QCYU/), [IGVFFI5769CDIM](/sequence-files/IGVFFI5769CDIM/), [IGVFFI7256NAKF](/sequence-files/IGVFFI7256NAKF/), [IGVFFI4700RBZU](/sequence-files/IGVFFI4700RBZU/), [IGVFFI9108JKFO](/sequence-files/IGVFFI9108JKFO/), [IGVFFI0101BUVS](/sequence-files/IGVFFI0101BUVS/), [IGVFFI2622TDFJ](/sequence-files/IGVFFI2622TDFJ/), [IGVFFI6897GKYL](/sequence-files/IGVFFI6897GKYL/), [IGVFFI5972PKDV](/sequence-files/IGVFFI5972PKDV/), [IGVFFI7762IALH](/sequence-files/IGVFFI7762IALH/), [IGVFFI3470ZROK](/sequence-files/IGVFFI3470ZROK/), [IGVFFI5954CAPT](/sequence-files/IGVFFI5954CAPT/), [IGVFFI0432GPRT](/sequence-files/IGVFFI0432GPRT/), [IGVFFI0067YXAS](/sequence-files/IGVFFI0067YXAS/), [IGVFFI2430FYVT](/sequence-files/IGVFFI2430FYVT/), [IGVFFI1429UHQV](/sequence-files/IGVFFI1429UHQV/), [IGVFFI8125BGTH](/sequence-files/IGVFFI8125BGTH/), [IGVFFI1975ZDMS](/sequence-files/IGVFFI1975ZDMS/), [IGVFFI9728SQIV](/sequence-files/IGVFFI9728SQIV/), [IGVFFI1495ULOM](/sequence-files/IGVFFI1495ULOM/), [IGVFFI1675XTZN](/sequence-files/IGVFFI1675XTZN/), [IGVFFI7440EWXZ](/sequence-files/IGVFFI7440EWXZ/), [IGVFFI5966TSUV](/sequence-files/IGVFFI5966TSUV/), [IGVFFI2754EDGI](/sequence-files/IGVFFI2754EDGI/), [IGVFFI9006OHQQ](/sequence-files/IGVFFI9006OHQQ/), [IGVFFI9890VGIB](/sequence-files/IGVFFI9890VGIB/), [IGVFFI8415WVOE](/sequence-files/IGVFFI8415WVOE/), [IGVFFI6984IMKC](/sequence-files/IGVFFI6984IMKC/), [IGVFFI4419NXZS](/sequence-files/IGVFFI4419NXZS/) 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/IGVFDS7995HXFV/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM4954YHLR](/in-vitro-systems/IGVFSM4954YHLR/) 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/IGVFSM4954YHLR/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM4954YHLR](/in-vitro-systems/IGVFSM4954YHLR/) 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/IGVFSM4954YHLR/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7995HXFV](/measurement-sets/IGVFDS7995HXFV/) 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/IGVFDS7995HXFV/"
}
]
},
"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": "2024-11-22T00:47:05.820374+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/IGVFFI0221UHWF/",
"accession": "IGVFFI0221UHWF",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T02:18:40.258026+00:00",
"file_format": "fastq",
"file_size": 5457041,
"href": "/sequence-files/IGVFFI0221UHWF/@@download/IGVFFI0221UHWF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/6fe6a41e-63c1-488e-83d1-1569dd9b05f8/IGVFFI0221UHWF.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-FFRep1-PCRRep1-BinC_S3_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8900RECT/",
"accession": "IGVFFI8900RECT",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T05:33:56.650515+00:00",
"file_format": "fastq",
"file_size": 5847207,
"href": "/sequence-files/IGVFFI8900RECT/@@download/IGVFFI8900RECT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/816b76b7-7908-443f-8d9b-8d7ffb33c425/IGVFFI8900RECT.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-FFRep1-PCRRep2-BinC_S27_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8548DYGM/",
"accession": "IGVFFI8548DYGM",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T05:42:36.653222+00:00",
"file_format": "fastq",
"file_size": 6950556,
"href": "/sequence-files/IGVFFI8548DYGM/@@download/IGVFFI8548DYGM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/b86b36cc-de3b-434c-b4f0-2318628af911/IGVFFI8548DYGM.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-FFRep1-PCRRep6-BinC_S123_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0579QCYU/",
"accession": "IGVFFI0579QCYU",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep5_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T05:40:34.135807+00:00",
"file_format": "fastq",
"file_size": 6863043,
"href": "/sequence-files/IGVFFI0579QCYU/@@download/IGVFFI0579QCYU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/573ef00a-c15e-486d-9d15-4f4c1caae33f/IGVFFI0579QCYU.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-FFRep1-PCRRep5-BinC_S99_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5769CDIM/",
"accession": "IGVFFI5769CDIM",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T05:36:25.338274+00:00",
"file_format": "fastq",
"file_size": 11382035,
"href": "/sequence-files/IGVFFI5769CDIM/@@download/IGVFFI5769CDIM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/dc4e99df-f87c-4120-ab51-812c8e4856c6/IGVFFI5769CDIM.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-FFRep1-PCRRep3-BinC_S51_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7256NAKF/",
"accession": "IGVFFI7256NAKF",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T05:38:30.661084+00:00",
"file_format": "fastq",
"file_size": 5806176,
"href": "/sequence-files/IGVFFI7256NAKF/@@download/IGVFFI7256NAKF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/8257fc6b-725f-43b7-bbe6-b2beb91b38fa/IGVFFI7256NAKF.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-FFRep1-PCRRep4-BinC_S75_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4700RBZU/",
"accession": "IGVFFI4700RBZU",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep7_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T05:44:29.658072+00:00",
"file_format": "fastq",
"file_size": 6788691,
"href": "/sequence-files/IGVFFI4700RBZU/@@download/IGVFFI4700RBZU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/bfab61f8-1cca-4933-8a4f-0e5acee0e65b/IGVFFI4700RBZU.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-FFRep1-PCRRep7-BinC_S147_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9108JKFO/",
"accession": "IGVFFI9108JKFO",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep8_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T05:46:27.279600+00:00",
"file_format": "fastq",
"file_size": 6807118,
"href": "/sequence-files/IGVFFI9108JKFO/@@download/IGVFFI9108JKFO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/c119430a-6a1d-48fb-af51-1c0d754b588b/IGVFFI9108JKFO.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-FFRep1-PCRRep8-BinC_S171_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0101BUVS/",
"accession": "IGVFFI0101BUVS",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep5_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:27:31.742325+00:00",
"file_format": "fastq",
"file_size": 9217845,
"href": "/sequence-files/IGVFFI0101BUVS/@@download/IGVFFI0101BUVS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/b82ee116-4479-4a8e-bb32-77b86ea39ab8/IGVFFI0101BUVS.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-FFRep1-PCRRep5-BinC_S99_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2622TDFJ/",
"accession": "IGVFFI2622TDFJ",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:23:54.875173+00:00",
"file_format": "fastq",
"file_size": 6425940,
"href": "/sequence-files/IGVFFI2622TDFJ/@@download/IGVFFI2622TDFJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/0b47e043-e3a6-4974-a516-7d13b70efeb1/IGVFFI2622TDFJ.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-FFRep1-PCRRep2-BinC_S27_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6897GKYL/",
"accession": "IGVFFI6897GKYL",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:26:19.205454+00:00",
"file_format": "fastq",
"file_size": 6331261,
"href": "/sequence-files/IGVFFI6897GKYL/@@download/IGVFFI6897GKYL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/1db60baa-22a8-430c-a055-dad4696a1312/IGVFFI6897GKYL.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-FFRep1-PCRRep4-BinC_S75_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5972PKDV/",
"accession": "IGVFFI5972PKDV",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:28:44.354101+00:00",
"file_format": "fastq",
"file_size": 9407902,
"href": "/sequence-files/IGVFFI5972PKDV/@@download/IGVFFI5972PKDV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/f5d2757a-6f63-4dfa-96fa-d4c3f57d211f/IGVFFI5972PKDV.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-FFRep1-PCRRep6-BinC_S123_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7762IALH/",
"accession": "IGVFFI7762IALH",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:31:13.001379+00:00",
"file_format": "fastq",
"file_size": 9153689,
"href": "/sequence-files/IGVFFI7762IALH/@@download/IGVFFI7762IALH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/68465113-86d9-4081-8520-a9b8704e732f/IGVFFI7762IALH.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-FFRep1-PCRRep8-BinC_S171_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3470ZROK/",
"accession": "IGVFFI3470ZROK",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep7_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:29:57.811676+00:00",
"file_format": "fastq",
"file_size": 9119489,
"href": "/sequence-files/IGVFFI3470ZROK/@@download/IGVFFI3470ZROK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/45bebbdf-40f1-4696-be03-ed124b17ac10/IGVFFI3470ZROK.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-FFRep1-PCRRep7-BinC_S147_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5954CAPT/",
"accession": "IGVFFI5954CAPT",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:22:42.364761+00:00",
"file_format": "fastq",
"file_size": 5958766,
"href": "/sequence-files/IGVFFI5954CAPT/@@download/IGVFFI5954CAPT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/2df3e2fa-e9bb-4888-9878-83fae3c30525/IGVFFI5954CAPT.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-FFRep1-PCRRep1-BinC_S3_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0432GPRT/",
"accession": "IGVFFI0432GPRT",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:25:07.039727+00:00",
"file_format": "fastq",
"file_size": 12354822,
"href": "/sequence-files/IGVFFI0432GPRT/@@download/IGVFFI0432GPRT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/0e2a2530-67d0-447d-9572-4ffb00fffbbd/IGVFFI0432GPRT.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-FFRep1-PCRRep3-BinC_S51_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0067YXAS/",
"accession": "IGVFFI0067YXAS",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep8_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:33:05.269402+00:00",
"file_format": "fastq",
"file_size": 2332576,
"href": "/sequence-files/IGVFFI0067YXAS/@@download/IGVFFI0067YXAS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/010167de-bee9-463e-bccb-8176c18bc6b5/IGVFFI0067YXAS.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-FFRep1-PCRRep8-BinC_S171_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2430FYVT/",
"accession": "IGVFFI2430FYVT",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:24:03.702620+00:00",
"file_format": "fastq",
"file_size": 1505263,
"href": "/sequence-files/IGVFFI2430FYVT/@@download/IGVFFI2430FYVT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/bc16b151-d59f-40d1-8079-c797615cf580/IGVFFI2430FYVT.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-FFRep1-PCRRep1-BinC_S3_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1429UHQV/",
"accession": "IGVFFI1429UHQV",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:27:39.263479+00:00",
"file_format": "fastq",
"file_size": 1617999,
"href": "/sequence-files/IGVFFI1429UHQV/@@download/IGVFFI1429UHQV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/3c223ff3-e692-43f8-9fc3-a25248ffe31b/IGVFFI1429UHQV.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-FFRep1-PCRRep4-BinC_S75_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8125BGTH/",
"accession": "IGVFFI8125BGTH",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep5_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:29:00.398869+00:00",
"file_format": "fastq",
"file_size": 2321883,
"href": "/sequence-files/IGVFFI8125BGTH/@@download/IGVFFI8125BGTH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/d87113fa-8000-4a87-9e4b-e0802409d158/IGVFFI8125BGTH.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-FFRep1-PCRRep5-BinC_S99_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1975ZDMS/",
"accession": "IGVFFI1975ZDMS",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:25:15.653469+00:00",
"file_format": "fastq",
"file_size": 1619973,
"href": "/sequence-files/IGVFFI1975ZDMS/@@download/IGVFFI1975ZDMS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/57cebb8e-e225-4637-a4e3-ed35fc37745e/IGVFFI1975ZDMS.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-FFRep1-PCRRep2-BinC_S27_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9728SQIV/",
"accession": "IGVFFI9728SQIV",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:26:27.156900+00:00",
"file_format": "fastq",
"file_size": 3041472,
"href": "/sequence-files/IGVFFI9728SQIV/@@download/IGVFFI9728SQIV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/e7ecff78-19e3-41c0-a789-2f89c70f2083/IGVFFI9728SQIV.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-FFRep1-PCRRep3-BinC_S51_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1495ULOM/",
"accession": "IGVFFI1495ULOM",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep6_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:30:21.665223+00:00",
"file_format": "fastq",
"file_size": 2325177,
"href": "/sequence-files/IGVFFI1495ULOM/@@download/IGVFFI1495ULOM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/a6db9ea9-a558-4d15-b0a4-17ac226e55b8/IGVFFI1495ULOM.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-FFRep1-PCRRep6-BinC_S123_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1675XTZN/",
"accession": "IGVFFI1675XTZN",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep7_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:31:42.402453+00:00",
"file_format": "fastq",
"file_size": 2246062,
"href": "/sequence-files/IGVFFI1675XTZN/@@download/IGVFFI1675XTZN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/23f019ab-2455-4b0d-ae3c-93639f34ada3/IGVFFI1675XTZN.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-FFRep1-PCRRep7-BinC_S147_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7440EWXZ/",
"accession": "IGVFFI7440EWXZ",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep5_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:31:06.277682+00:00",
"file_format": "fastq",
"file_size": 1975296,
"href": "/sequence-files/IGVFFI7440EWXZ/@@download/IGVFFI7440EWXZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/ec75e28f-00a1-4eb4-b9fe-b1a6fb290f73/IGVFFI7440EWXZ.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-FFRep1-PCRRep5-BinC_S99_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5966TSUV/",
"accession": "IGVFFI5966TSUV",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:25:57.753760+00:00",
"file_format": "fastq",
"file_size": 1470843,
"href": "/sequence-files/IGVFFI5966TSUV/@@download/IGVFFI5966TSUV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/9912c97c-7ebe-41e2-a513-b898ac7aed87/IGVFFI5966TSUV.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-FFRep1-PCRRep1-BinC_S3_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2754EDGI/",
"accession": "IGVFFI2754EDGI",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep3_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:28:30.158164+00:00",
"file_format": "fastq",
"file_size": 3029274,
"href": "/sequence-files/IGVFFI2754EDGI/@@download/IGVFFI2754EDGI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/5970c9b0-2bb0-44c0-8892-d4021876c07c/IGVFFI2754EDGI.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-FFRep1-PCRRep3-BinC_S51_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9006OHQQ/",
"accession": "IGVFFI9006OHQQ",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep6_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:32:25.416209+00:00",
"file_format": "fastq",
"file_size": 1996228,
"href": "/sequence-files/IGVFFI9006OHQQ/@@download/IGVFFI9006OHQQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/045d33f6-15f2-4db4-a2db-6ae3f7a4bc8e/IGVFFI9006OHQQ.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-FFRep1-PCRRep6-BinC_S123_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9890VGIB/",
"accession": "IGVFFI9890VGIB",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep7_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:33:46.870904+00:00",
"file_format": "fastq",
"file_size": 1954971,
"href": "/sequence-files/IGVFFI9890VGIB/@@download/IGVFFI9890VGIB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/1deec9a0-a2d0-4c0c-a9f8-29ebf9b85114/IGVFFI9890VGIB.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-FFRep1-PCRRep7-BinC_S147_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8415WVOE/",
"accession": "IGVFFI8415WVOE",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:27:14.181203+00:00",
"file_format": "fastq",
"file_size": 1579160,
"href": "/sequence-files/IGVFFI8415WVOE/@@download/IGVFFI8415WVOE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/b24561d3-bb0e-4231-8b15-474b614029b2/IGVFFI8415WVOE.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-FFRep1-PCRRep2-BinC_S27_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6984IMKC/",
"accession": "IGVFFI6984IMKC",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:29:48.289155+00:00",
"file_format": "fastq",
"file_size": 1574443,
"href": "/sequence-files/IGVFFI6984IMKC/@@download/IGVFFI6984IMKC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/2eea88f6-058d-4505-a015-ef471825d6d7/IGVFFI6984IMKC.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-FFRep1-PCRRep4-BinC_S75_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4419NXZS/",
"accession": "IGVFFI4419NXZS",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC-PCRRep8_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:35:07.579610+00:00",
"file_format": "fastq",
"file_size": 1961332,
"href": "/sequence-files/IGVFFI4419NXZS/@@download/IGVFFI4419NXZS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/20ccdba0-7041-46cb-8c9e-9de50f3284b9/IGVFFI4419NXZS.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-FFRep1-PCRRep8-BinC_S171_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/IGVFSM4954YHLR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4954YHLR",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinC"
],
"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 51-75% 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": "2024-11-22T02:18:40.258026+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": "f89c61d9-a5b3-462e-a04b-5c39b2db99b4"
}