{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4412KNQI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4412KNQI",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-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 [IGVFDS4412KNQI](/measurement-sets/IGVFDS4412KNQI/) has sequence file(s) [IGVFFI2910CSOZ](/sequence-files/IGVFFI2910CSOZ/), [IGVFFI1248PWUP](/sequence-files/IGVFFI1248PWUP/), [IGVFFI7922BZCQ](/sequence-files/IGVFFI7922BZCQ/), [IGVFFI7339DDFP](/sequence-files/IGVFFI7339DDFP/), [IGVFFI6046OPSN](/sequence-files/IGVFFI6046OPSN/), [IGVFFI6343FOJK](/sequence-files/IGVFFI6343FOJK/), [IGVFFI8987VMHI](/sequence-files/IGVFFI8987VMHI/), [IGVFFI7477WSWI](/sequence-files/IGVFFI7477WSWI/), [IGVFFI1016QHAL](/sequence-files/IGVFFI1016QHAL/), [IGVFFI2327NUYR](/sequence-files/IGVFFI2327NUYR/), [IGVFFI0785HVSM](/sequence-files/IGVFFI0785HVSM/), [IGVFFI9363URER](/sequence-files/IGVFFI9363URER/), [IGVFFI2610ZXCO](/sequence-files/IGVFFI2610ZXCO/), [IGVFFI3569FRMY](/sequence-files/IGVFFI3569FRMY/), [IGVFFI3605KDPL](/sequence-files/IGVFFI3605KDPL/), [IGVFFI1401GOIJ](/sequence-files/IGVFFI1401GOIJ/) 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/IGVFDS4412KNQI/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4412KNQI](/measurement-sets/IGVFDS4412KNQI/) has sequence file(s): [IGVFFI2910CSOZ](/sequence-files/IGVFFI2910CSOZ/), [IGVFFI1248PWUP](/sequence-files/IGVFFI1248PWUP/), [IGVFFI7922BZCQ](/sequence-files/IGVFFI7922BZCQ/), [IGVFFI7339DDFP](/sequence-files/IGVFFI7339DDFP/), [IGVFFI6046OPSN](/sequence-files/IGVFFI6046OPSN/), [IGVFFI6343FOJK](/sequence-files/IGVFFI6343FOJK/), [IGVFFI8987VMHI](/sequence-files/IGVFFI8987VMHI/), [IGVFFI7477WSWI](/sequence-files/IGVFFI7477WSWI/), [IGVFFI1016QHAL](/sequence-files/IGVFFI1016QHAL/), [IGVFFI2327NUYR](/sequence-files/IGVFFI2327NUYR/), [IGVFFI0785HVSM](/sequence-files/IGVFFI0785HVSM/), [IGVFFI9363URER](/sequence-files/IGVFFI9363URER/), [IGVFFI2610ZXCO](/sequence-files/IGVFFI2610ZXCO/), [IGVFFI3569FRMY](/sequence-files/IGVFFI3569FRMY/), [IGVFFI3605KDPL](/sequence-files/IGVFFI3605KDPL/), [IGVFFI1401GOIJ](/sequence-files/IGVFFI1401GOIJ/) 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/IGVFDS4412KNQI/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4412KNQI](/measurement-sets/IGVFDS4412KNQI/) 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/IGVFDS4412KNQI/"
}
]
},
"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": "2024-12-10T22:37:09.681175+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/IGVFFI2910CSOZ/",
"accession": "IGVFFI2910CSOZ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinC-PCRrep4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-10T23:56:16.410185+00:00",
"file_format": "fastq",
"file_size": 12304258,
"href": "/sequence-files/IGVFFI2910CSOZ/@@download/IGVFFI2910CSOZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/10/5cb02d7b-d6a2-420e-942e-a453a3b561ae/IGVFFI2910CSOZ.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-BioRep1-FFrep1-BinC-PCRrep4_S809_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1248PWUP/",
"accession": "IGVFFI1248PWUP",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-10T23:47:55.432535+00:00",
"file_format": "fastq",
"file_size": 19236893,
"href": "/sequence-files/IGVFFI1248PWUP/@@download/IGVFFI1248PWUP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/10/3df7badd-601c-4f93-acc2-d522a428d07d/IGVFFI1248PWUP.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-BioRep1-FFrep1-BinC-PCRrep1_S773_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7922BZCQ/",
"accession": "IGVFFI7922BZCQ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-10T23:50:54.565138+00:00",
"file_format": "fastq",
"file_size": 7948919,
"href": "/sequence-files/IGVFFI7922BZCQ/@@download/IGVFFI7922BZCQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/10/70299a10-aa06-4b7d-aefb-e5a4d10e6fe9/IGVFFI7922BZCQ.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-BioRep1-FFrep1-BinC-PCRrep2_S785_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7339DDFP/",
"accession": "IGVFFI7339DDFP",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinC-PCRrep3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-10T23:53:49.209738+00:00",
"file_format": "fastq",
"file_size": 5306782,
"href": "/sequence-files/IGVFFI7339DDFP/@@download/IGVFFI7339DDFP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/10/77648352-7fd5-4523-b3b2-a3a6dd27e62d/IGVFFI7339DDFP.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-BioRep1-FFrep1-BinC-PCRrep3_S797_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6046OPSN/",
"accession": "IGVFFI6046OPSN",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinC-PCRrep3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T16:58:26.879529+00:00",
"file_format": "fastq",
"file_size": 4854396,
"href": "/sequence-files/IGVFFI6046OPSN/@@download/IGVFFI6046OPSN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/7630a939-10a4-4f16-907f-186feffa4fb7/IGVFFI6046OPSN.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-BioRep1-FFrep1-BinC-PCRrep3_S797_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6343FOJK/",
"accession": "IGVFFI6343FOJK",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinC-PCRrep4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T16:59:44.714742+00:00",
"file_format": "fastq",
"file_size": 10807575,
"href": "/sequence-files/IGVFFI6343FOJK/@@download/IGVFFI6343FOJK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/1cf779ed-6877-47fd-913f-c989e0ccf39a/IGVFFI6343FOJK.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-BioRep1-FFrep1-BinC-PCRrep4_S809_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8987VMHI/",
"accession": "IGVFFI8987VMHI",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T16:56:55.514966+00:00",
"file_format": "fastq",
"file_size": 7171060,
"href": "/sequence-files/IGVFFI8987VMHI/@@download/IGVFFI8987VMHI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/75bc9995-591c-4378-b467-94b12d6f9a10/IGVFFI8987VMHI.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-BioRep1-FFrep1-BinC-PCRrep2_S785_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7477WSWI/",
"accession": "IGVFFI7477WSWI",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T16:55:26.358328+00:00",
"file_format": "fastq",
"file_size": 17213100,
"href": "/sequence-files/IGVFFI7477WSWI/@@download/IGVFFI7477WSWI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/f6c42eeb-eb7b-4f38-b441-10a88ffc9261/IGVFFI7477WSWI.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-BioRep1-FFrep1-BinC-PCRrep1_S773_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1016QHAL/",
"accession": "IGVFFI1016QHAL",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T22:45:01.673166+00:00",
"file_format": "fastq",
"file_size": 2947880,
"href": "/sequence-files/IGVFFI1016QHAL/@@download/IGVFFI1016QHAL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/5c02395b-e5a7-49ce-b95e-1ea5d5ebd170/IGVFFI1016QHAL.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-BioRep1-FFrep1-BinC-PCRrep2_S785_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2327NUYR/",
"accession": "IGVFFI2327NUYR",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinC-PCRrep4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T20:37:56.290742+00:00",
"file_format": "fastq",
"file_size": 4264865,
"href": "/sequence-files/IGVFFI2327NUYR/@@download/IGVFFI2327NUYR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/040ccb7b-3d98-4437-a19a-22e777ea0b7b/IGVFFI2327NUYR.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-BioRep1-FFrep1-BinC-PCRrep4_S809_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0785HVSM/",
"accession": "IGVFFI0785HVSM",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T20:29:33.085741+00:00",
"file_format": "fastq",
"file_size": 6466691,
"href": "/sequence-files/IGVFFI0785HVSM/@@download/IGVFFI0785HVSM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/7b8fea0a-7642-4a95-b48e-5c176e1e2536/IGVFFI0785HVSM.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-BioRep1-FFrep1-BinC-PCRrep1_S773_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9363URER/",
"accession": "IGVFFI9363URER",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T20:32:30.956944+00:00",
"file_format": "fastq",
"file_size": 2736955,
"href": "/sequence-files/IGVFFI9363URER/@@download/IGVFFI9363URER.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/0f17e1e4-5d1f-4260-9c83-cd41a1ef7214/IGVFFI9363URER.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-BioRep1-FFrep1-BinC-PCRrep2_S785_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2610ZXCO/",
"accession": "IGVFFI2610ZXCO",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinC-PCRrep3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T20:35:23.669608+00:00",
"file_format": "fastq",
"file_size": 1734340,
"href": "/sequence-files/IGVFFI2610ZXCO/@@download/IGVFFI2610ZXCO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/a50f1e3c-d75b-4fd6-afa3-111ea3a1921a/IGVFFI2610ZXCO.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-BioRep1-FFrep1-BinC-PCRrep3_S797_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3569FRMY/",
"accession": "IGVFFI3569FRMY",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinC-PCRrep3_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T22:48:09.851818+00:00",
"file_format": "fastq",
"file_size": 1870433,
"href": "/sequence-files/IGVFFI3569FRMY/@@download/IGVFFI3569FRMY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/a8f2de63-2e7c-4739-9a0e-8c383d336cdb/IGVFFI3569FRMY.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-BioRep1-FFrep1-BinC-PCRrep3_S797_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3605KDPL/",
"accession": "IGVFFI3605KDPL",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinC-PCRrep4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T22:50:42.792291+00:00",
"file_format": "fastq",
"file_size": 4501816,
"href": "/sequence-files/IGVFFI3605KDPL/@@download/IGVFFI3605KDPL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/e06f2978-5f87-4f21-a9b7-15dda2e6eeab/IGVFFI3605KDPL.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-BioRep1-FFrep1-BinC-PCRrep4_S809_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1401GOIJ/",
"accession": "IGVFFI1401GOIJ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T22:42:16.844966+00:00",
"file_format": "fastq",
"file_size": 7091384,
"href": "/sequence-files/IGVFFI1401GOIJ/@@download/IGVFFI1401GOIJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/4c874248-123b-4c7b-831a-d27ed0c2dfad/IGVFFI1401GOIJ.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-BioRep1-FFrep1-BinC-PCRrep1_S773_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/IGVFSM9715ABLU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9715ABLU",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-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": "2024-12-10T23:47:55.432535+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": "7dbaa85f-24a2-405c-ba1b-5f98016f13c7"
}