{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3671LLGR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3671LLGR",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinA_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 [IGVFDS3671LLGR](/measurement-sets/IGVFDS3671LLGR/) has sequence file(s) [IGVFFI0680OMKD](/sequence-files/IGVFFI0680OMKD/), [IGVFFI0688DEHE](/sequence-files/IGVFFI0688DEHE/), [IGVFFI7724RGJB](/sequence-files/IGVFFI7724RGJB/), [IGVFFI7438BODM](/sequence-files/IGVFFI7438BODM/), [IGVFFI1973HJRG](/sequence-files/IGVFFI1973HJRG/), [IGVFFI6901STBZ](/sequence-files/IGVFFI6901STBZ/), [IGVFFI7520DXYK](/sequence-files/IGVFFI7520DXYK/), [IGVFFI4922YXNX](/sequence-files/IGVFFI4922YXNX/), [IGVFFI4138DYOI](/sequence-files/IGVFFI4138DYOI/), [IGVFFI7556TJQR](/sequence-files/IGVFFI7556TJQR/), [IGVFFI2320SVSF](/sequence-files/IGVFFI2320SVSF/), [IGVFFI2941VGUJ](/sequence-files/IGVFFI2941VGUJ/), [IGVFFI8101VHTK](/sequence-files/IGVFFI8101VHTK/), [IGVFFI7232PSDF](/sequence-files/IGVFFI7232PSDF/), [IGVFFI4388VEHJ](/sequence-files/IGVFFI4388VEHJ/), [IGVFFI0012JHHF](/sequence-files/IGVFFI0012JHHF/) 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/IGVFDS3671LLGR/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3671LLGR](/measurement-sets/IGVFDS3671LLGR/) has sequence file(s): [IGVFFI0680OMKD](/sequence-files/IGVFFI0680OMKD/), [IGVFFI0688DEHE](/sequence-files/IGVFFI0688DEHE/), [IGVFFI7724RGJB](/sequence-files/IGVFFI7724RGJB/), [IGVFFI7438BODM](/sequence-files/IGVFFI7438BODM/), [IGVFFI1973HJRG](/sequence-files/IGVFFI1973HJRG/), [IGVFFI6901STBZ](/sequence-files/IGVFFI6901STBZ/), [IGVFFI7520DXYK](/sequence-files/IGVFFI7520DXYK/), [IGVFFI4922YXNX](/sequence-files/IGVFFI4922YXNX/), [IGVFFI4138DYOI](/sequence-files/IGVFFI4138DYOI/), [IGVFFI7556TJQR](/sequence-files/IGVFFI7556TJQR/), [IGVFFI2320SVSF](/sequence-files/IGVFFI2320SVSF/), [IGVFFI2941VGUJ](/sequence-files/IGVFFI2941VGUJ/), [IGVFFI8101VHTK](/sequence-files/IGVFFI8101VHTK/), [IGVFFI7232PSDF](/sequence-files/IGVFFI7232PSDF/), [IGVFFI4388VEHJ](/sequence-files/IGVFFI4388VEHJ/), [IGVFFI0012JHHF](/sequence-files/IGVFFI0012JHHF/) 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/IGVFDS3671LLGR/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3671LLGR](/measurement-sets/IGVFDS3671LLGR/) 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/IGVFDS3671LLGR/"
}
]
},
"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": "2024-12-10T22:36:48.512752+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/IGVFFI0680OMKD/",
"accession": "IGVFFI0680OMKD",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinA-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-10T23:46:41.679350+00:00",
"file_format": "fastq",
"file_size": 26513627,
"href": "/sequence-files/IGVFFI0680OMKD/@@download/IGVFFI0680OMKD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/10/9d40d9c8-30ae-4ecd-a538-ea4493992358/IGVFFI0680OMKD.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-BinA-PCRrep1_S771_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0688DEHE/",
"accession": "IGVFFI0688DEHE",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinA-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-10T23:49:44.536863+00:00",
"file_format": "fastq",
"file_size": 8809881,
"href": "/sequence-files/IGVFFI0688DEHE/@@download/IGVFFI0688DEHE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/10/26ba9673-6192-4bb8-9851-8f9b5d36ac53/IGVFFI0688DEHE.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-BinA-PCRrep2_S783_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7724RGJB/",
"accession": "IGVFFI7724RGJB",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinA-PCRrep3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-10T23:52:38.183319+00:00",
"file_format": "fastq",
"file_size": 6954469,
"href": "/sequence-files/IGVFFI7724RGJB/@@download/IGVFFI7724RGJB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/10/aa3cb709-edf2-4241-aa04-f59df357514a/IGVFFI7724RGJB.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-BinA-PCRrep3_S795_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7438BODM/",
"accession": "IGVFFI7438BODM",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinA-PCRrep4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-10T23:55:03.553346+00:00",
"file_format": "fastq",
"file_size": 18011891,
"href": "/sequence-files/IGVFFI7438BODM/@@download/IGVFFI7438BODM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/10/a861ce0b-835f-4f0d-a234-f2eb8dcf0e3f/IGVFFI7438BODM.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-BinA-PCRrep4_S807_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1973HJRG/",
"accession": "IGVFFI1973HJRG",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinA-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T16:54:48.567189+00:00",
"file_format": "fastq",
"file_size": 23285644,
"href": "/sequence-files/IGVFFI1973HJRG/@@download/IGVFFI1973HJRG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/eb632fed-19f0-4698-82a2-4a6dbb021109/IGVFFI1973HJRG.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-BinA-PCRrep1_S771_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6901STBZ/",
"accession": "IGVFFI6901STBZ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinA-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T16:56:20.318495+00:00",
"file_format": "fastq",
"file_size": 7712760,
"href": "/sequence-files/IGVFFI6901STBZ/@@download/IGVFFI6901STBZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/cf187e54-d74e-41d3-aca1-f2b229027b95/IGVFFI6901STBZ.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-BinA-PCRrep2_S783_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7520DXYK/",
"accession": "IGVFFI7520DXYK",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinA-PCRrep3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T16:57:50.611038+00:00",
"file_format": "fastq",
"file_size": 6330690,
"href": "/sequence-files/IGVFFI7520DXYK/@@download/IGVFFI7520DXYK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/3a547858-97b5-4e35-83cf-d87514dacb5e/IGVFFI7520DXYK.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-BinA-PCRrep3_S795_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4922YXNX/",
"accession": "IGVFFI4922YXNX",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinA-PCRrep4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T16:59:04.569996+00:00",
"file_format": "fastq",
"file_size": 16063009,
"href": "/sequence-files/IGVFFI4922YXNX/@@download/IGVFFI4922YXNX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/c0c011af-6878-4f77-9ed8-d4f95398336a/IGVFFI4922YXNX.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-BinA-PCRrep4_S807_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4138DYOI/",
"accession": "IGVFFI4138DYOI",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinA-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T20:28:25.718177+00:00",
"file_format": "fastq",
"file_size": 10135533,
"href": "/sequence-files/IGVFFI4138DYOI/@@download/IGVFFI4138DYOI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/3e7c0a03-1756-4abd-a0b5-c0dd58f81185/IGVFFI4138DYOI.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-BinA-PCRrep1_S771_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7556TJQR/",
"accession": "IGVFFI7556TJQR",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinA-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T22:40:58.987430+00:00",
"file_format": "fastq",
"file_size": 9678596,
"href": "/sequence-files/IGVFFI7556TJQR/@@download/IGVFFI7556TJQR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/2e8ebc22-848c-4b68-9fd5-4429345e375d/IGVFFI7556TJQR.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-BinA-PCRrep1_S771_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2320SVSF/",
"accession": "IGVFFI2320SVSF",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinA-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T20:31:17.367300+00:00",
"file_format": "fastq",
"file_size": 3173966,
"href": "/sequence-files/IGVFFI2320SVSF/@@download/IGVFFI2320SVSF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/a34c0592-0d4a-4cc1-9585-3df5f34f253d/IGVFFI2320SVSF.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-BinA-PCRrep2_S783_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2941VGUJ/",
"accession": "IGVFFI2941VGUJ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinA-PCRrep4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T20:36:37.525523+00:00",
"file_format": "fastq",
"file_size": 6302550,
"href": "/sequence-files/IGVFFI2941VGUJ/@@download/IGVFFI2941VGUJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/53e2c908-5ec0-440b-97c7-1a42f084cff3/IGVFFI2941VGUJ.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-BinA-PCRrep4_S807_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8101VHTK/",
"accession": "IGVFFI8101VHTK",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinA-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T22:43:50.452437+00:00",
"file_format": "fastq",
"file_size": 3361667,
"href": "/sequence-files/IGVFFI8101VHTK/@@download/IGVFFI8101VHTK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/8ecb5fd4-7fe8-4910-a943-47e3bd583ac4/IGVFFI8101VHTK.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-BinA-PCRrep2_S783_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7232PSDF/",
"accession": "IGVFFI7232PSDF",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinA-PCRrep3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T20:34:12.929877+00:00",
"file_format": "fastq",
"file_size": 2595372,
"href": "/sequence-files/IGVFFI7232PSDF/@@download/IGVFFI7232PSDF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/bb77e295-ae40-4126-b5db-a7ae9c9b6331/IGVFFI7232PSDF.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-BinA-PCRrep3_S795_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4388VEHJ/",
"accession": "IGVFFI4388VEHJ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinA-PCRrep4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T22:49:23.255027+00:00",
"file_format": "fastq",
"file_size": 6321168,
"href": "/sequence-files/IGVFFI4388VEHJ/@@download/IGVFFI4388VEHJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/d1b06268-b33a-4f16-9625-30199ffdd943/IGVFFI4388VEHJ.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-BinA-PCRrep4_S807_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0012JHHF/",
"accession": "IGVFFI0012JHHF",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinA-PCRrep3_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T22:46:57.970548+00:00",
"file_format": "fastq",
"file_size": 2610786,
"href": "/sequence-files/IGVFFI0012JHHF/@@download/IGVFFI0012JHHF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/5c452fbc-4210-43fd-9461-9e8723da08b5/IGVFFI0012JHHF.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-BinA-PCRrep3_S795_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/IGVFSM9724FSDM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9724FSDM",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-BinA"
],
"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 0-25% 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": "2024-12-10T23:46:41.679350+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": "07dfbf8f-7440-46e6-9ab9-9766a8c37687"
}