{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7310MDWF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7310MDWF",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-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 [IGVFDS7310MDWF](/measurement-sets/IGVFDS7310MDWF/) has sequence file(s) [IGVFFI2501PMCZ](/sequence-files/IGVFFI2501PMCZ/), [IGVFFI3303NYCL](/sequence-files/IGVFFI3303NYCL/), [IGVFFI5132UCTK](/sequence-files/IGVFFI5132UCTK/), [IGVFFI3793ZIGN](/sequence-files/IGVFFI3793ZIGN/), [IGVFFI3441INRD](/sequence-files/IGVFFI3441INRD/), [IGVFFI5994FRPK](/sequence-files/IGVFFI5994FRPK/), [IGVFFI8961LTUC](/sequence-files/IGVFFI8961LTUC/), [IGVFFI2279QTVE](/sequence-files/IGVFFI2279QTVE/), [IGVFFI0689IVJP](/sequence-files/IGVFFI0689IVJP/), [IGVFFI2560IAJV](/sequence-files/IGVFFI2560IAJV/), [IGVFFI6050VEED](/sequence-files/IGVFFI6050VEED/), [IGVFFI6550YREV](/sequence-files/IGVFFI6550YREV/), [IGVFFI1575WZQE](/sequence-files/IGVFFI1575WZQE/), [IGVFFI0050OEKF](/sequence-files/IGVFFI0050OEKF/), [IGVFFI3439UFPF](/sequence-files/IGVFFI3439UFPF/), [IGVFFI4346OXSU](/sequence-files/IGVFFI4346OXSU/) 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/IGVFDS7310MDWF/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7310MDWF](/measurement-sets/IGVFDS7310MDWF/) has sequence file(s): [IGVFFI2501PMCZ](/sequence-files/IGVFFI2501PMCZ/), [IGVFFI3303NYCL](/sequence-files/IGVFFI3303NYCL/), [IGVFFI5132UCTK](/sequence-files/IGVFFI5132UCTK/), [IGVFFI3793ZIGN](/sequence-files/IGVFFI3793ZIGN/), [IGVFFI3441INRD](/sequence-files/IGVFFI3441INRD/), [IGVFFI5994FRPK](/sequence-files/IGVFFI5994FRPK/), [IGVFFI8961LTUC](/sequence-files/IGVFFI8961LTUC/), [IGVFFI2279QTVE](/sequence-files/IGVFFI2279QTVE/), [IGVFFI0689IVJP](/sequence-files/IGVFFI0689IVJP/), [IGVFFI2560IAJV](/sequence-files/IGVFFI2560IAJV/), [IGVFFI6050VEED](/sequence-files/IGVFFI6050VEED/), [IGVFFI6550YREV](/sequence-files/IGVFFI6550YREV/), [IGVFFI1575WZQE](/sequence-files/IGVFFI1575WZQE/), [IGVFFI0050OEKF](/sequence-files/IGVFFI0050OEKF/), [IGVFFI3439UFPF](/sequence-files/IGVFFI3439UFPF/), [IGVFFI4346OXSU](/sequence-files/IGVFFI4346OXSU/) 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/IGVFDS7310MDWF/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7310MDWF](/measurement-sets/IGVFDS7310MDWF/) 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/IGVFDS7310MDWF/"
}
]
},
"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/IGVFDS8210FQOO/",
"accession": "IGVFDS8210FQOO",
"aliases": [
"jesse-engreitz:THP1-PE2_Exp7_PPIF_5SpliceSite-IndividualVariantExp_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-12-10T22:39:36.664366+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/IGVFFI2501PMCZ/",
"accession": "IGVFFI2501PMCZ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T00:23:04.042389+00:00",
"file_format": "fastq",
"file_size": 14803604,
"href": "/sequence-files/IGVFFI2501PMCZ/@@download/IGVFFI2501PMCZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/0c95d00f-fe01-4942-8d53-358fa27264e9/IGVFFI2501PMCZ.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinC-PCRrep2_S833_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3303NYCL/",
"accession": "IGVFFI3303NYCL",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T00:19:59.748074+00:00",
"file_format": "fastq",
"file_size": 31741870,
"href": "/sequence-files/IGVFFI3303NYCL/@@download/IGVFFI3303NYCL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/8f6fa831-04e2-4fa9-9eaa-d05459aad642/IGVFFI3303NYCL.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinC-PCRrep1_S821_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5132UCTK/",
"accession": "IGVFFI5132UCTK",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinC-PCRrep3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T00:26:11.294223+00:00",
"file_format": "fastq",
"file_size": 26324525,
"href": "/sequence-files/IGVFFI5132UCTK/@@download/IGVFFI5132UCTK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/85c3fefe-ed87-4ba6-9534-fec3a52a65f9/IGVFFI5132UCTK.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinC-PCRrep3_S845_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3793ZIGN/",
"accession": "IGVFFI3793ZIGN",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinC-PCRrep4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T00:28:37.548128+00:00",
"file_format": "fastq",
"file_size": 23189789,
"href": "/sequence-files/IGVFFI3793ZIGN/@@download/IGVFFI3793ZIGN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/f24e53bf-d9ab-4725-8c6e-f6a1a7faf3bb/IGVFFI3793ZIGN.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinC-PCRrep4_S857_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3441INRD/",
"accession": "IGVFFI3441INRD",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinC-PCRrep4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T17:20:29.019118+00:00",
"file_format": "fastq",
"file_size": 20780322,
"href": "/sequence-files/IGVFFI3441INRD/@@download/IGVFFI3441INRD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/2d5d0653-1b90-4522-a11c-3eb6e61293fb/IGVFFI3441INRD.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinC-PCRrep4_S857_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5994FRPK/",
"accession": "IGVFFI5994FRPK",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T17:14:37.090757+00:00",
"file_format": "fastq",
"file_size": 27524726,
"href": "/sequence-files/IGVFFI5994FRPK/@@download/IGVFFI5994FRPK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/0723ea58-1e24-4824-bbca-aa2794771bde/IGVFFI5994FRPK.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinC-PCRrep1_S821_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8961LTUC/",
"accession": "IGVFFI8961LTUC",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T17:16:38.976969+00:00",
"file_format": "fastq",
"file_size": 13387958,
"href": "/sequence-files/IGVFFI8961LTUC/@@download/IGVFFI8961LTUC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/c57b0f37-217e-40f3-9724-f966a11ea009/IGVFFI8961LTUC.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinC-PCRrep2_S833_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2279QTVE/",
"accession": "IGVFFI2279QTVE",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinC-PCRrep3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T17:18:46.548491+00:00",
"file_format": "fastq",
"file_size": 22353118,
"href": "/sequence-files/IGVFFI2279QTVE/@@download/IGVFFI2279QTVE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/46c9dfe3-ef40-4a76-855a-0096faa1c82c/IGVFFI2279QTVE.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinC-PCRrep3_S845_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0689IVJP/",
"accession": "IGVFFI0689IVJP",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinC-PCRrep3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T21:08:40.258909+00:00",
"file_format": "fastq",
"file_size": 9320406,
"href": "/sequence-files/IGVFFI0689IVJP/@@download/IGVFFI0689IVJP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/57cc5b1c-1399-4a5a-833f-74d488f7268e/IGVFFI0689IVJP.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinC-PCRrep3_S845_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2560IAJV/",
"accession": "IGVFFI2560IAJV",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T21:02:32.067431+00:00",
"file_format": "fastq",
"file_size": 10592272,
"href": "/sequence-files/IGVFFI2560IAJV/@@download/IGVFFI2560IAJV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/7d98af42-2017-49e0-8011-b56bd57b39a3/IGVFFI2560IAJV.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinC-PCRrep1_S821_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6050VEED/",
"accession": "IGVFFI6050VEED",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T23:15:16.732331+00:00",
"file_format": "fastq",
"file_size": 11076894,
"href": "/sequence-files/IGVFFI6050VEED/@@download/IGVFFI6050VEED.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/5d44a43b-ee72-4e30-8ba5-b9b3e09295a7/IGVFFI6050VEED.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinC-PCRrep1_S821_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6550YREV/",
"accession": "IGVFFI6550YREV",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinC-PCRrep4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T21:11:13.346913+00:00",
"file_format": "fastq",
"file_size": 7467287,
"href": "/sequence-files/IGVFFI6550YREV/@@download/IGVFFI6550YREV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/f862508e-a0fb-41fa-a31e-d0130ae19e9d/IGVFFI6550YREV.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinC-PCRrep4_S857_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1575WZQE/",
"accession": "IGVFFI1575WZQE",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T23:18:17.137083+00:00",
"file_format": "fastq",
"file_size": 5294076,
"href": "/sequence-files/IGVFFI1575WZQE/@@download/IGVFFI1575WZQE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/15f7dca4-9026-46a6-9939-886d35ed4d7b/IGVFFI1575WZQE.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinC-PCRrep2_S833_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0050OEKF/",
"accession": "IGVFFI0050OEKF",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T21:05:34.280102+00:00",
"file_format": "fastq",
"file_size": 4856043,
"href": "/sequence-files/IGVFFI0050OEKF/@@download/IGVFFI0050OEKF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/40f9c65a-88d5-4d68-a2a3-08d3aa5666c1/IGVFFI0050OEKF.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinC-PCRrep2_S833_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3439UFPF/",
"accession": "IGVFFI3439UFPF",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinC-PCRrep4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T23:23:52.561193+00:00",
"file_format": "fastq",
"file_size": 7942524,
"href": "/sequence-files/IGVFFI3439UFPF/@@download/IGVFFI3439UFPF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/cc69c181-ef31-4a42-b26f-970f5a44f9f4/IGVFFI3439UFPF.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinC-PCRrep4_S857_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4346OXSU/",
"accession": "IGVFFI4346OXSU",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinC-PCRrep3_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T23:21:18.895457+00:00",
"file_format": "fastq",
"file_size": 9140968,
"href": "/sequence-files/IGVFFI4346OXSU/@@download/IGVFFI4346OXSU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/ef5665b0-faa9-4bb4-ad04-08b268f3bf57/IGVFFI4346OXSU.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinC-PCRrep3_S845_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8267JJHO/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"preferred_assay_title": "Variant-EFFECTS",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1873QXGA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1873QXGA",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-BinC"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS9097TEUZ/",
"accession": "IGVFDS9097TEUZ",
"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": "2024-12-11T00:19:59.748074+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": "85b8d254-11c2-41d2-b0e2-4cff71230c5d"
}