{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9847QETL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9847QETL",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-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 [IGVFDS9847QETL](/measurement-sets/IGVFDS9847QETL/) has sequence file(s) [IGVFFI1790JEZQ](/sequence-files/IGVFFI1790JEZQ/), [IGVFFI4279BUWA](/sequence-files/IGVFFI4279BUWA/), [IGVFFI4984IWXQ](/sequence-files/IGVFFI4984IWXQ/), [IGVFFI0937NRCQ](/sequence-files/IGVFFI0937NRCQ/), [IGVFFI2356KKEJ](/sequence-files/IGVFFI2356KKEJ/), [IGVFFI8761WUFP](/sequence-files/IGVFFI8761WUFP/), [IGVFFI0953QUVO](/sequence-files/IGVFFI0953QUVO/), [IGVFFI3361XQMY](/sequence-files/IGVFFI3361XQMY/), [IGVFFI8163WNDL](/sequence-files/IGVFFI8163WNDL/), [IGVFFI4901BIQH](/sequence-files/IGVFFI4901BIQH/), [IGVFFI1639LURN](/sequence-files/IGVFFI1639LURN/), [IGVFFI6743YESN](/sequence-files/IGVFFI6743YESN/), [IGVFFI7617VSWJ](/sequence-files/IGVFFI7617VSWJ/), [IGVFFI5839XIKA](/sequence-files/IGVFFI5839XIKA/), [IGVFFI6153XCRV](/sequence-files/IGVFFI6153XCRV/), [IGVFFI8828ZMNH](/sequence-files/IGVFFI8828ZMNH/), [IGVFFI6755BECY](/sequence-files/IGVFFI6755BECY/), [IGVFFI5641DSJE](/sequence-files/IGVFFI5641DSJE/), [IGVFFI7535MHLB](/sequence-files/IGVFFI7535MHLB/), [IGVFFI3177XMBX](/sequence-files/IGVFFI3177XMBX/), [IGVFFI4451YDXP](/sequence-files/IGVFFI4451YDXP/), [IGVFFI5157UWLH](/sequence-files/IGVFFI5157UWLH/), [IGVFFI6536RHXM](/sequence-files/IGVFFI6536RHXM/), [IGVFFI6705RTCQ](/sequence-files/IGVFFI6705RTCQ/), [IGVFFI9257KJGZ](/sequence-files/IGVFFI9257KJGZ/), [IGVFFI7788ZFAU](/sequence-files/IGVFFI7788ZFAU/), [IGVFFI8810QOML](/sequence-files/IGVFFI8810QOML/), [IGVFFI1331WVTY](/sequence-files/IGVFFI1331WVTY/), [IGVFFI6781RUUB](/sequence-files/IGVFFI6781RUUB/), [IGVFFI8907GAUZ](/sequence-files/IGVFFI8907GAUZ/), [IGVFFI2697URSE](/sequence-files/IGVFFI2697URSE/), [IGVFFI8781LIHK](/sequence-files/IGVFFI8781LIHK/) 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/IGVFDS9847QETL/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9847QETL](/measurement-sets/IGVFDS9847QETL/) has sequence file(s): [IGVFFI1790JEZQ](/sequence-files/IGVFFI1790JEZQ/), [IGVFFI4279BUWA](/sequence-files/IGVFFI4279BUWA/), [IGVFFI4984IWXQ](/sequence-files/IGVFFI4984IWXQ/), [IGVFFI0937NRCQ](/sequence-files/IGVFFI0937NRCQ/), [IGVFFI2356KKEJ](/sequence-files/IGVFFI2356KKEJ/), [IGVFFI8761WUFP](/sequence-files/IGVFFI8761WUFP/), [IGVFFI0953QUVO](/sequence-files/IGVFFI0953QUVO/), [IGVFFI3361XQMY](/sequence-files/IGVFFI3361XQMY/), [IGVFFI8163WNDL](/sequence-files/IGVFFI8163WNDL/), [IGVFFI4901BIQH](/sequence-files/IGVFFI4901BIQH/), [IGVFFI1639LURN](/sequence-files/IGVFFI1639LURN/), [IGVFFI6743YESN](/sequence-files/IGVFFI6743YESN/), [IGVFFI7617VSWJ](/sequence-files/IGVFFI7617VSWJ/), [IGVFFI5839XIKA](/sequence-files/IGVFFI5839XIKA/), [IGVFFI6153XCRV](/sequence-files/IGVFFI6153XCRV/), [IGVFFI8828ZMNH](/sequence-files/IGVFFI8828ZMNH/), [IGVFFI6755BECY](/sequence-files/IGVFFI6755BECY/), [IGVFFI5641DSJE](/sequence-files/IGVFFI5641DSJE/), [IGVFFI7535MHLB](/sequence-files/IGVFFI7535MHLB/), [IGVFFI3177XMBX](/sequence-files/IGVFFI3177XMBX/), [IGVFFI4451YDXP](/sequence-files/IGVFFI4451YDXP/), [IGVFFI5157UWLH](/sequence-files/IGVFFI5157UWLH/), [IGVFFI6536RHXM](/sequence-files/IGVFFI6536RHXM/), [IGVFFI6705RTCQ](/sequence-files/IGVFFI6705RTCQ/), [IGVFFI9257KJGZ](/sequence-files/IGVFFI9257KJGZ/), [IGVFFI7788ZFAU](/sequence-files/IGVFFI7788ZFAU/), [IGVFFI8810QOML](/sequence-files/IGVFFI8810QOML/), [IGVFFI1331WVTY](/sequence-files/IGVFFI1331WVTY/), [IGVFFI6781RUUB](/sequence-files/IGVFFI6781RUUB/), [IGVFFI8907GAUZ](/sequence-files/IGVFFI8907GAUZ/), [IGVFFI2697URSE](/sequence-files/IGVFFI2697URSE/), [IGVFFI8781LIHK](/sequence-files/IGVFFI8781LIHK/) 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/IGVFDS9847QETL/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM1409FVBR](/in-vitro-systems/IGVFSM1409FVBR/) 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/IGVFSM1409FVBR/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM1409FVBR](/in-vitro-systems/IGVFSM1409FVBR/) 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/IGVFSM1409FVBR/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9847QETL](/measurement-sets/IGVFDS9847QETL/) 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/IGVFDS9847QETL/"
}
]
},
"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": "2024-11-22T00:47:53.257430+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/IGVFFI1790JEZQ/",
"accession": "IGVFFI1790JEZQ",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T06:07:35.217273+00:00",
"file_format": "fastq",
"file_size": 12224016,
"href": "/sequence-files/IGVFFI1790JEZQ/@@download/IGVFFI1790JEZQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/e7f27da7-ebe0-4026-a797-05645596bbd3/IGVFFI1790JEZQ.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-BinC_S59_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4279BUWA/",
"accession": "IGVFFI4279BUWA",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T06:03:40.228415+00:00",
"file_format": "fastq",
"file_size": 5501577,
"href": "/sequence-files/IGVFFI4279BUWA/@@download/IGVFFI4279BUWA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/5fd7ba60-abe0-4e8b-b0d8-cffcb438fce9/IGVFFI4279BUWA.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-BinC_S11_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4984IWXQ/",
"accession": "IGVFFI4984IWXQ",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T06:13:36.070937+00:00",
"file_format": "fastq",
"file_size": 6760891,
"href": "/sequence-files/IGVFFI4984IWXQ/@@download/IGVFFI4984IWXQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/acbc2f31-4f9d-4d39-9c83-27b9b12236a8/IGVFFI4984IWXQ.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-BinC_S131_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0937NRCQ/",
"accession": "IGVFFI0937NRCQ",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T06:05:41.527461+00:00",
"file_format": "fastq",
"file_size": 6124785,
"href": "/sequence-files/IGVFFI0937NRCQ/@@download/IGVFFI0937NRCQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/73e57d1e-3986-490b-8918-82566e0d7dee/IGVFFI0937NRCQ.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-BinC_S35_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2356KKEJ/",
"accession": "IGVFFI2356KKEJ",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep8_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T06:17:20.901233+00:00",
"file_format": "fastq",
"file_size": 7065858,
"href": "/sequence-files/IGVFFI2356KKEJ/@@download/IGVFFI2356KKEJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/cc3625b2-99a4-4849-818c-cb8f0b55efc7/IGVFFI2356KKEJ.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-BinC_S179_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8761WUFP/",
"accession": "IGVFFI8761WUFP",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T06:09:28.065620+00:00",
"file_format": "fastq",
"file_size": 6079700,
"href": "/sequence-files/IGVFFI8761WUFP/@@download/IGVFFI8761WUFP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/46612754-b6d7-4199-8941-fa8273a49e76/IGVFFI8761WUFP.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-BinC_S83_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0953QUVO/",
"accession": "IGVFFI0953QUVO",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep5_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T06:11:35.441496+00:00",
"file_format": "fastq",
"file_size": 6641191,
"href": "/sequence-files/IGVFFI0953QUVO/@@download/IGVFFI0953QUVO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/1e3fe049-3010-4eb6-8685-5a3ecade3acf/IGVFFI0953QUVO.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-BinC_S107_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3361XQMY/",
"accession": "IGVFFI3361XQMY",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep7_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T06:15:28.562856+00:00",
"file_format": "fastq",
"file_size": 6324399,
"href": "/sequence-files/IGVFFI3361XQMY/@@download/IGVFFI3361XQMY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/26fae358-811c-4d4b-a93c-749d8f76d398/IGVFFI3361XQMY.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-BinC_S155_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8163WNDL/",
"accession": "IGVFFI8163WNDL",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:42:44.943827+00:00",
"file_format": "fastq",
"file_size": 5945128,
"href": "/sequence-files/IGVFFI8163WNDL/@@download/IGVFFI8163WNDL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/8add4cc1-7544-478c-b7e0-aadda4693e0e/IGVFFI8163WNDL.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-BinC_S11_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4901BIQH/",
"accession": "IGVFFI4901BIQH",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:44:07.550018+00:00",
"file_format": "fastq",
"file_size": 6596621,
"href": "/sequence-files/IGVFFI4901BIQH/@@download/IGVFFI4901BIQH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/504db93a-dd90-4f9c-8199-500e3c35423d/IGVFFI4901BIQH.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-BinC_S35_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1639LURN/",
"accession": "IGVFFI1639LURN",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:51:35.179250+00:00",
"file_format": "fastq",
"file_size": 9355269,
"href": "/sequence-files/IGVFFI1639LURN/@@download/IGVFFI1639LURN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/8bbfc9d1-9195-4a80-8511-1f061293e66a/IGVFFI1639LURN.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-BinC_S179_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6743YESN/",
"accession": "IGVFFI6743YESN",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:45:28.111364+00:00",
"file_format": "fastq",
"file_size": 13228678,
"href": "/sequence-files/IGVFFI6743YESN/@@download/IGVFFI6743YESN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/4261c068-76db-476b-9d80-d47f32ea16c8/IGVFFI6743YESN.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-BinC_S59_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7617VSWJ/",
"accession": "IGVFFI7617VSWJ",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep5_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:47:55.408331+00:00",
"file_format": "fastq",
"file_size": 8853914,
"href": "/sequence-files/IGVFFI7617VSWJ/@@download/IGVFFI7617VSWJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/411edb20-9352-4b8b-93a0-c1dadae01c10/IGVFFI7617VSWJ.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-BinC_S107_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5839XIKA/",
"accession": "IGVFFI5839XIKA",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:46:40.357206+00:00",
"file_format": "fastq",
"file_size": 6522357,
"href": "/sequence-files/IGVFFI5839XIKA/@@download/IGVFFI5839XIKA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/dbeb531f-933c-4339-ab94-87bd5fc30620/IGVFFI5839XIKA.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-BinC_S83_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6153XCRV/",
"accession": "IGVFFI6153XCRV",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:49:09.644203+00:00",
"file_format": "fastq",
"file_size": 8959768,
"href": "/sequence-files/IGVFFI6153XCRV/@@download/IGVFFI6153XCRV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/8bbf5746-5c23-4650-8c4f-67d224b54adb/IGVFFI6153XCRV.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-BinC_S131_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8828ZMNH/",
"accession": "IGVFFI8828ZMNH",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep7_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T18:50:22.241033+00:00",
"file_format": "fastq",
"file_size": 8463191,
"href": "/sequence-files/IGVFFI8828ZMNH/@@download/IGVFFI8828ZMNH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/674834c1-f035-4aa0-8142-f3f432a27bbd/IGVFFI8828ZMNH.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-BinC_S155_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6755BECY/",
"accession": "IGVFFI6755BECY",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep5_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:49:11.177440+00:00",
"file_format": "fastq",
"file_size": 2275173,
"href": "/sequence-files/IGVFFI6755BECY/@@download/IGVFFI6755BECY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/b487e999-52fa-42a5-9f44-9a423dbc06ff/IGVFFI6755BECY.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-BinC_S107_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5641DSJE/",
"accession": "IGVFFI5641DSJE",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep7_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:51:34.441176+00:00",
"file_format": "fastq",
"file_size": 2125355,
"href": "/sequence-files/IGVFFI5641DSJE/@@download/IGVFFI5641DSJE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/b773d526-826f-4f7b-b659-00ad4cdd8e51/IGVFFI5641DSJE.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-BinC_S155_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7535MHLB/",
"accession": "IGVFFI7535MHLB",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:46:47.571761+00:00",
"file_format": "fastq",
"file_size": 3244077,
"href": "/sequence-files/IGVFFI7535MHLB/@@download/IGVFFI7535MHLB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/062f73e5-500e-4360-9744-5c0c654b64b8/IGVFFI7535MHLB.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-BinC_S59_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3177XMBX/",
"accession": "IGVFFI3177XMBX",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:47:58.299190+00:00",
"file_format": "fastq",
"file_size": 1676476,
"href": "/sequence-files/IGVFFI3177XMBX/@@download/IGVFFI3177XMBX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/e2dda627-0970-40c8-972f-cbabbc95d588/IGVFFI3177XMBX.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-BinC_S83_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4451YDXP/",
"accession": "IGVFFI4451YDXP",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:45:37.061396+00:00",
"file_format": "fastq",
"file_size": 1702449,
"href": "/sequence-files/IGVFFI4451YDXP/@@download/IGVFFI4451YDXP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/f41ceb9f-0296-4f0a-98a2-14da084e6d6b/IGVFFI4451YDXP.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-BinC_S35_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5157UWLH/",
"accession": "IGVFFI5157UWLH",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep8_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:52:46.865982+00:00",
"file_format": "fastq",
"file_size": 2357686,
"href": "/sequence-files/IGVFFI5157UWLH/@@download/IGVFFI5157UWLH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/3dd2b634-ca11-46b6-8e66-2df12ec0ee32/IGVFFI5157UWLH.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-BinC_S179_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6536RHXM/",
"accession": "IGVFFI6536RHXM",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:44:25.591998+00:00",
"file_format": "fastq",
"file_size": 1532412,
"href": "/sequence-files/IGVFFI6536RHXM/@@download/IGVFFI6536RHXM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/aa39e0ce-16e1-4228-933c-115813ba7f77/IGVFFI6536RHXM.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-BinC_S11_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6705RTCQ/",
"accession": "IGVFFI6705RTCQ",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep6_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T19:50:22.721061+00:00",
"file_format": "fastq",
"file_size": 2323215,
"href": "/sequence-files/IGVFFI6705RTCQ/@@download/IGVFFI6705RTCQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/f782c2b1-454c-4fde-a42a-81efe5e975a9/IGVFFI6705RTCQ.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-BinC_S131_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9257KJGZ/",
"accession": "IGVFFI9257KJGZ",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep3_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:49:15.818322+00:00",
"file_format": "fastq",
"file_size": 3224108,
"href": "/sequence-files/IGVFFI9257KJGZ/@@download/IGVFFI9257KJGZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/1cfe43a1-a4ef-498c-8984-0d9ee95db30b/IGVFFI9257KJGZ.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-BinC_S59_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7788ZFAU/",
"accession": "IGVFFI7788ZFAU",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:46:43.934122+00:00",
"file_format": "fastq",
"file_size": 1486353,
"href": "/sequence-files/IGVFFI7788ZFAU/@@download/IGVFFI7788ZFAU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/da151bb9-56ee-43e3-8ad7-fa64e9c92e50/IGVFFI7788ZFAU.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-BinC_S11_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8810QOML/",
"accession": "IGVFFI8810QOML",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:47:58.728003+00:00",
"file_format": "fastq",
"file_size": 1647454,
"href": "/sequence-files/IGVFFI8810QOML/@@download/IGVFFI8810QOML.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/fecf3497-e7fe-41fb-8556-2b2abea2b6a8/IGVFFI8810QOML.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-BinC_S35_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1331WVTY/",
"accession": "IGVFFI1331WVTY",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep6_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:53:18.019075+00:00",
"file_format": "fastq",
"file_size": 1956371,
"href": "/sequence-files/IGVFFI1331WVTY/@@download/IGVFFI1331WVTY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/0fad68a4-c7ed-4313-8c72-e25e265eaec5/IGVFFI1331WVTY.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-BinC_S131_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6781RUUB/",
"accession": "IGVFFI6781RUUB",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep8_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:56:22.538430+00:00",
"file_format": "fastq",
"file_size": 2021149,
"href": "/sequence-files/IGVFFI6781RUUB/@@download/IGVFFI6781RUUB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/7ad30c33-2221-4560-a569-2864a823c94d/IGVFFI6781RUUB.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-BinC_S179_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8907GAUZ/",
"accession": "IGVFFI8907GAUZ",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:50:32.423975+00:00",
"file_format": "fastq",
"file_size": 1630339,
"href": "/sequence-files/IGVFFI8907GAUZ/@@download/IGVFFI8907GAUZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/d7250432-7fda-4b1f-b36c-2fb3b66ef4db/IGVFFI8907GAUZ.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-BinC_S83_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2697URSE/",
"accession": "IGVFFI2697URSE",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep5_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:51:53.233091+00:00",
"file_format": "fastq",
"file_size": 1902149,
"href": "/sequence-files/IGVFFI2697URSE/@@download/IGVFFI2697URSE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/ff807622-f604-400c-a7e5-a112fe52dc0b/IGVFFI2697URSE.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-BinC_S107_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8781LIHK/",
"accession": "IGVFFI8781LIHK",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinC-PCRRep7_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-22T20:54:47.885218+00:00",
"file_format": "fastq",
"file_size": 1831784,
"href": "/sequence-files/IGVFFI8781LIHK/@@download/IGVFFI8781LIHK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/22/30d070cc-bb41-439c-b6ce-fc42e8d9c28f/IGVFFI8781LIHK.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-BinC_S155_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/IGVFSM1409FVBR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1409FVBR",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-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": "2024-11-22T06:03:40.228415+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": "469ec986-b776-4394-917c-c76c4e5bf1b8"
}