{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4694FAVN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4694FAVN",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-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 [IGVFDS4694FAVN](/measurement-sets/IGVFDS4694FAVN/) has sequence file(s) [IGVFFI4151TSOK](/sequence-files/IGVFFI4151TSOK/), [IGVFFI4379GMEP](/sequence-files/IGVFFI4379GMEP/), [IGVFFI9930WUIZ](/sequence-files/IGVFFI9930WUIZ/), [IGVFFI1476ZJZF](/sequence-files/IGVFFI1476ZJZF/), [IGVFFI8909WVZG](/sequence-files/IGVFFI8909WVZG/), [IGVFFI9224TOJU](/sequence-files/IGVFFI9224TOJU/), [IGVFFI4232DJAB](/sequence-files/IGVFFI4232DJAB/), [IGVFFI6544QUQI](/sequence-files/IGVFFI6544QUQI/), [IGVFFI8571SLBR](/sequence-files/IGVFFI8571SLBR/), [IGVFFI5471EOUP](/sequence-files/IGVFFI5471EOUP/), [IGVFFI5635TFSW](/sequence-files/IGVFFI5635TFSW/), [IGVFFI7137ZISV](/sequence-files/IGVFFI7137ZISV/), [IGVFFI0917MUPV](/sequence-files/IGVFFI0917MUPV/), [IGVFFI3914VIZS](/sequence-files/IGVFFI3914VIZS/), [IGVFFI8067CEPU](/sequence-files/IGVFFI8067CEPU/), [IGVFFI7876DIIQ](/sequence-files/IGVFFI7876DIIQ/) 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/IGVFDS4694FAVN/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4694FAVN](/measurement-sets/IGVFDS4694FAVN/) has sequence file(s): [IGVFFI4151TSOK](/sequence-files/IGVFFI4151TSOK/), [IGVFFI4379GMEP](/sequence-files/IGVFFI4379GMEP/), [IGVFFI9930WUIZ](/sequence-files/IGVFFI9930WUIZ/), [IGVFFI1476ZJZF](/sequence-files/IGVFFI1476ZJZF/), [IGVFFI8909WVZG](/sequence-files/IGVFFI8909WVZG/), [IGVFFI9224TOJU](/sequence-files/IGVFFI9224TOJU/), [IGVFFI4232DJAB](/sequence-files/IGVFFI4232DJAB/), [IGVFFI6544QUQI](/sequence-files/IGVFFI6544QUQI/), [IGVFFI8571SLBR](/sequence-files/IGVFFI8571SLBR/), [IGVFFI5471EOUP](/sequence-files/IGVFFI5471EOUP/), [IGVFFI5635TFSW](/sequence-files/IGVFFI5635TFSW/), [IGVFFI7137ZISV](/sequence-files/IGVFFI7137ZISV/), [IGVFFI0917MUPV](/sequence-files/IGVFFI0917MUPV/), [IGVFFI3914VIZS](/sequence-files/IGVFFI3914VIZS/), [IGVFFI8067CEPU](/sequence-files/IGVFFI8067CEPU/), [IGVFFI7876DIIQ](/sequence-files/IGVFFI7876DIIQ/) 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/IGVFDS4694FAVN/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4694FAVN](/measurement-sets/IGVFDS4694FAVN/) 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/IGVFDS4694FAVN/"
}
]
},
"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/IGVFDS0861MZYT/",
"accession": "IGVFDS0861MZYT",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-PE2_Exp6_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-12-01T19:58:11.398612+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4151TSOK/",
"accession": "IGVFFI4151TSOK",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-BinC-PCRrep4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T20:56:05.160827+00:00",
"file_format": "fastq",
"file_size": 13182733,
"href": "/sequence-files/IGVFFI4151TSOK/@@download/IGVFFI4151TSOK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/d0b44b5e-d786-44a7-a9a6-feebee7741e1/IGVFFI4151TSOK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinC-PCRrep4_S749_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4379GMEP/",
"accession": "IGVFFI4379GMEP",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T21:35:58.244701+00:00",
"file_format": "fastq",
"file_size": 7019082,
"href": "/sequence-files/IGVFFI4379GMEP/@@download/IGVFFI4379GMEP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/36bd4921-bbf3-49ad-8e93-98e0af458aab/IGVFFI4379GMEP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinC-PCRrep2_S725_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9930WUIZ/",
"accession": "IGVFFI9930WUIZ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T20:50:22.804308+00:00",
"file_format": "fastq",
"file_size": 7773364,
"href": "/sequence-files/IGVFFI9930WUIZ/@@download/IGVFFI9930WUIZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/4dcecc9a-1fda-4338-a747-28ac07d99fb8/IGVFFI9930WUIZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinC-PCRrep2_S725_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1476ZJZF/",
"accession": "IGVFFI1476ZJZF",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-BinC-PCRrep4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:34:09.390382+00:00",
"file_format": "fastq",
"file_size": 4181067,
"href": "/sequence-files/IGVFFI1476ZJZF/@@download/IGVFFI1476ZJZF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/19d8a80c-a205-4603-b445-548f9d716dc9/IGVFFI1476ZJZF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinC-PCRrep4_S749_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8909WVZG/",
"accession": "IGVFFI8909WVZG",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T20:47:00.737156+00:00",
"file_format": "fastq",
"file_size": 16479600,
"href": "/sequence-files/IGVFFI8909WVZG/@@download/IGVFFI8909WVZG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/b1317562-4b9a-4c13-a3f1-eacf1817ab5c/IGVFFI8909WVZG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinC-PCRrep1_S713_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9224TOJU/",
"accession": "IGVFFI9224TOJU",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-BinC-PCRrep3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T20:53:49.547895+00:00",
"file_format": "fastq",
"file_size": 5719643,
"href": "/sequence-files/IGVFFI9224TOJU/@@download/IGVFFI9224TOJU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/702202b3-1609-4fca-a587-555206c5668f/IGVFFI9224TOJU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinC-PCRrep3_S737_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4232DJAB/",
"accession": "IGVFFI4232DJAB",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T21:32:06.683714+00:00",
"file_format": "fastq",
"file_size": 14511385,
"href": "/sequence-files/IGVFFI4232DJAB/@@download/IGVFFI4232DJAB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/c2aea015-6b00-42b9-b844-c37a088814f9/IGVFFI4232DJAB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinC-PCRrep1_S713_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6544QUQI/",
"accession": "IGVFFI6544QUQI",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-BinC-PCRrep3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T21:41:37.288701+00:00",
"file_format": "fastq",
"file_size": 5435176,
"href": "/sequence-files/IGVFFI6544QUQI/@@download/IGVFFI6544QUQI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/166cbca4-4bf9-465c-be46-1cf777c7e766/IGVFFI6544QUQI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinC-PCRrep3_S737_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8571SLBR/",
"accession": "IGVFFI8571SLBR",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-BinC-PCRrep4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T21:44:35.908783+00:00",
"file_format": "fastq",
"file_size": 11698386,
"href": "/sequence-files/IGVFFI8571SLBR/@@download/IGVFFI8571SLBR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/f9bfce7e-6a63-49f0-8044-0eebf9cc4de4/IGVFFI8571SLBR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinC-PCRrep4_S749_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5471EOUP/",
"accession": "IGVFFI5471EOUP",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:22:22.244975+00:00",
"file_format": "fastq",
"file_size": 5508232,
"href": "/sequence-files/IGVFFI5471EOUP/@@download/IGVFFI5471EOUP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/d2cdd259-9fcd-4887-a14e-c3739df3d6d6/IGVFFI5471EOUP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinC-PCRrep1_S713_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5635TFSW/",
"accession": "IGVFFI5635TFSW",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:27:34.616332+00:00",
"file_format": "fastq",
"file_size": 2957270,
"href": "/sequence-files/IGVFFI5635TFSW/@@download/IGVFFI5635TFSW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/794b2749-3b03-4f93-8df2-b20e470ef824/IGVFFI5635TFSW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinC-PCRrep2_S725_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7137ZISV/",
"accession": "IGVFFI7137ZISV",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T23:11:12.345435+00:00",
"file_format": "fastq",
"file_size": 5249354,
"href": "/sequence-files/IGVFFI7137ZISV/@@download/IGVFFI7137ZISV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/bcc0fbca-778e-42d8-97cd-108a66a5bcb4/IGVFFI7137ZISV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinC-PCRrep1_S713_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0917MUPV/",
"accession": "IGVFFI0917MUPV",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-BinC-PCRrep3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:31:43.172305+00:00",
"file_format": "fastq",
"file_size": 1870548,
"href": "/sequence-files/IGVFFI0917MUPV/@@download/IGVFFI0917MUPV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/8aa7f2d2-ef91-4734-a1c5-04bd1b819918/IGVFFI0917MUPV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinC-PCRrep3_S737_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3914VIZS/",
"accession": "IGVFFI3914VIZS",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T23:14:35.229076+00:00",
"file_format": "fastq",
"file_size": 2349031,
"href": "/sequence-files/IGVFFI3914VIZS/@@download/IGVFFI3914VIZS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/54db244d-0ac7-49ce-ad21-4224b9581ab2/IGVFFI3914VIZS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinC-PCRrep2_S725_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8067CEPU/",
"accession": "IGVFFI8067CEPU",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-BinC-PCRrep4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T23:20:17.725937+00:00",
"file_format": "fastq",
"file_size": 4101915,
"href": "/sequence-files/IGVFFI8067CEPU/@@download/IGVFFI8067CEPU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/899bef0d-60d0-4809-8e1f-2869aa72ecfe/IGVFFI8067CEPU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinC-PCRrep4_S749_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7876DIIQ/",
"accession": "IGVFFI7876DIIQ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-BinC-PCRrep3_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T23:17:59.520654+00:00",
"file_format": "fastq",
"file_size": 1619440,
"href": "/sequence-files/IGVFFI7876DIIQ/@@download/IGVFFI7876DIIQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/1da39cd6-5254-4651-ba7d-85faf1062d51/IGVFFI7876DIIQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinC-PCRrep3_S737_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7090INDM/"
],
"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/IGVFSM6632JLXQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6632JLXQ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep2-BinC"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS5639ITBS/",
"accession": "IGVFDS5639ITBS",
"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_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 51-75% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-12-01T20:47:00.737156+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"status": "released",
"symbol": "PPIF",
"synonyms": [
"rotamase F",
"CYP3",
"cyclophilin F",
"mitochondrial cyclophilin",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"CypD",
"Cyp-D",
"cyclophilin 3",
"cyclophilin D",
"CyP-M",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIase F"
]
}
],
"uuid": "3fe17fc9-027e-402a-b969-71ac5f13a8ec"
}