{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7842TVPS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7842TVPS",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-BinD_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 [IGVFDS7842TVPS](/measurement-sets/IGVFDS7842TVPS/) has sequence file(s) [IGVFFI9471CRAN](/sequence-files/IGVFFI9471CRAN/), [IGVFFI0381HDGO](/sequence-files/IGVFFI0381HDGO/), [IGVFFI0598LOHQ](/sequence-files/IGVFFI0598LOHQ/), [IGVFFI1386AMQI](/sequence-files/IGVFFI1386AMQI/), [IGVFFI5000OEFD](/sequence-files/IGVFFI5000OEFD/), [IGVFFI4684GBNU](/sequence-files/IGVFFI4684GBNU/), [IGVFFI7243EGPL](/sequence-files/IGVFFI7243EGPL/), [IGVFFI2104XTPC](/sequence-files/IGVFFI2104XTPC/), [IGVFFI9859ZAKZ](/sequence-files/IGVFFI9859ZAKZ/), [IGVFFI2179RHHI](/sequence-files/IGVFFI2179RHHI/), [IGVFFI2449HSCI](/sequence-files/IGVFFI2449HSCI/), [IGVFFI5237ZBNW](/sequence-files/IGVFFI5237ZBNW/), [IGVFFI1413PBWH](/sequence-files/IGVFFI1413PBWH/), [IGVFFI1089IXXN](/sequence-files/IGVFFI1089IXXN/), [IGVFFI6417LBMF](/sequence-files/IGVFFI6417LBMF/), [IGVFFI3192YGUU](/sequence-files/IGVFFI3192YGUU/) 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/IGVFDS7842TVPS/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7842TVPS](/measurement-sets/IGVFDS7842TVPS/) has sequence file(s): [IGVFFI9471CRAN](/sequence-files/IGVFFI9471CRAN/), [IGVFFI0381HDGO](/sequence-files/IGVFFI0381HDGO/), [IGVFFI0598LOHQ](/sequence-files/IGVFFI0598LOHQ/), [IGVFFI1386AMQI](/sequence-files/IGVFFI1386AMQI/), [IGVFFI5000OEFD](/sequence-files/IGVFFI5000OEFD/), [IGVFFI4684GBNU](/sequence-files/IGVFFI4684GBNU/), [IGVFFI7243EGPL](/sequence-files/IGVFFI7243EGPL/), [IGVFFI2104XTPC](/sequence-files/IGVFFI2104XTPC/), [IGVFFI9859ZAKZ](/sequence-files/IGVFFI9859ZAKZ/), [IGVFFI2179RHHI](/sequence-files/IGVFFI2179RHHI/), [IGVFFI2449HSCI](/sequence-files/IGVFFI2449HSCI/), [IGVFFI5237ZBNW](/sequence-files/IGVFFI5237ZBNW/), [IGVFFI1413PBWH](/sequence-files/IGVFFI1413PBWH/), [IGVFFI1089IXXN](/sequence-files/IGVFFI1089IXXN/), [IGVFFI6417LBMF](/sequence-files/IGVFFI6417LBMF/), [IGVFFI3192YGUU](/sequence-files/IGVFFI3192YGUU/) 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/IGVFDS7842TVPS/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7842TVPS](/measurement-sets/IGVFDS7842TVPS/) 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/IGVFDS7842TVPS/"
}
]
},
"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": "2024-12-01T19:58:54.196558+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/IGVFFI9471CRAN/",
"accession": "IGVFFI9471CRAN",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-BinD-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T23:36:17.753737+00:00",
"file_format": "fastq",
"file_size": 3724632,
"href": "/sequence-files/IGVFFI9471CRAN/@@download/IGVFFI9471CRAN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/894bcdd3-5dd1-49c6-9016-778bc1b3d247/IGVFFI9471CRAN.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-BioRep2-FFrep2-BinD-PCRrep2_S762_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0381HDGO/",
"accession": "IGVFFI0381HDGO",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-BinD-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:01:38.930730+00:00",
"file_format": "fastq",
"file_size": 9001990,
"href": "/sequence-files/IGVFFI0381HDGO/@@download/IGVFFI0381HDGO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/4576c9c5-8d1b-4b1c-b8f6-6fba3c9dbe1d/IGVFFI0381HDGO.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-BioRep2-FFrep2-BinD-PCRrep1_S758_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0598LOHQ/",
"accession": "IGVFFI0598LOHQ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-BinD-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:04:29.324703+00:00",
"file_format": "fastq",
"file_size": 10397377,
"href": "/sequence-files/IGVFFI0598LOHQ/@@download/IGVFFI0598LOHQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/501f78f5-fd62-41e8-8337-d0f2b13b7ff5/IGVFFI0598LOHQ.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-BioRep2-FFrep2-BinD-PCRrep2_S762_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1386AMQI/",
"accession": "IGVFFI1386AMQI",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-BinD-PCRrep3_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T21:15:11.013537+00:00",
"file_format": "fastq",
"file_size": 13364958,
"href": "/sequence-files/IGVFFI1386AMQI/@@download/IGVFFI1386AMQI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/78cf0478-82c3-4fa1-9ce5-27709c93f7b1/IGVFFI1386AMQI.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-BioRep2-FFrep2-BinD-PCRrep3_S766_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5000OEFD/",
"accession": "IGVFFI5000OEFD",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-BinD-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T21:09:32.620772+00:00",
"file_format": "fastq",
"file_size": 10146848,
"href": "/sequence-files/IGVFFI5000OEFD/@@download/IGVFFI5000OEFD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/aaa44b1a-057f-414a-88dd-65eac6d7466e/IGVFFI5000OEFD.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-BioRep2-FFrep2-BinD-PCRrep1_S758_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4684GBNU/",
"accession": "IGVFFI4684GBNU",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-BinD-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T21:12:14.212614+00:00",
"file_format": "fastq",
"file_size": 11523513,
"href": "/sequence-files/IGVFFI4684GBNU/@@download/IGVFFI4684GBNU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/bd926d72-e13f-4c21-a996-3ea1c988bd98/IGVFFI4684GBNU.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-BioRep2-FFrep2-BinD-PCRrep2_S762_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7243EGPL/",
"accession": "IGVFFI7243EGPL",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-BinD-PCRrep4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T21:17:47.285620+00:00",
"file_format": "fastq",
"file_size": 23133910,
"href": "/sequence-files/IGVFFI7243EGPL/@@download/IGVFFI7243EGPL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/69f762bc-2c51-4ec4-8aef-b01710814fa7/IGVFFI7243EGPL.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-BioRep2-FFrep2-BinD-PCRrep4_S770_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2104XTPC/",
"accession": "IGVFFI2104XTPC",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-BinD-PCRrep4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:09:36.259541+00:00",
"file_format": "fastq",
"file_size": 20717012,
"href": "/sequence-files/IGVFFI2104XTPC/@@download/IGVFFI2104XTPC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/cb27c619-d8c3-4bc9-8aea-b5dfe24161d8/IGVFFI2104XTPC.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-BioRep2-FFrep2-BinD-PCRrep4_S770_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9859ZAKZ/",
"accession": "IGVFFI9859ZAKZ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-BinD-PCRrep4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:57:56.294638+00:00",
"file_format": "fastq",
"file_size": 7510004,
"href": "/sequence-files/IGVFFI9859ZAKZ/@@download/IGVFFI9859ZAKZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/a77a56d1-d56e-4582-9cf7-c4b9e8bb3a11/IGVFFI9859ZAKZ.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-BioRep2-FFrep2-BinD-PCRrep4_S770_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2179RHHI/",
"accession": "IGVFFI2179RHHI",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-BinD-PCRrep3_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T23:39:18.773261+00:00",
"file_format": "fastq",
"file_size": 4389725,
"href": "/sequence-files/IGVFFI2179RHHI/@@download/IGVFFI2179RHHI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/8f05ae23-c296-4bd7-bbc3-e781a1d9dafc/IGVFFI2179RHHI.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-BioRep2-FFrep2-BinD-PCRrep3_S766_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2449HSCI/",
"accession": "IGVFFI2449HSCI",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-BinD-PCRrep3_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:07:19.083382+00:00",
"file_format": "fastq",
"file_size": 11889410,
"href": "/sequence-files/IGVFFI2449HSCI/@@download/IGVFFI2449HSCI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/c989c443-580d-41fb-81aa-f7bcba151071/IGVFFI2449HSCI.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-BioRep2-FFrep2-BinD-PCRrep3_S766_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5237ZBNW/",
"accession": "IGVFFI5237ZBNW",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-BinD-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:52:45.367012+00:00",
"file_format": "fastq",
"file_size": 3854466,
"href": "/sequence-files/IGVFFI5237ZBNW/@@download/IGVFFI5237ZBNW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/2cb2b91d-cb40-47a8-89ec-42eae4b0e6a5/IGVFFI5237ZBNW.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-BioRep2-FFrep2-BinD-PCRrep2_S762_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1413PBWH/",
"accession": "IGVFFI1413PBWH",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-BinD-PCRrep3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:55:34.697004+00:00",
"file_format": "fastq",
"file_size": 5195211,
"href": "/sequence-files/IGVFFI1413PBWH/@@download/IGVFFI1413PBWH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/98c34535-cc9d-40b7-9746-5880e930b796/IGVFFI1413PBWH.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-BioRep2-FFrep2-BinD-PCRrep3_S766_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1089IXXN/",
"accession": "IGVFFI1089IXXN",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-BinD-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:49:58.248437+00:00",
"file_format": "fastq",
"file_size": 3652985,
"href": "/sequence-files/IGVFFI1089IXXN/@@download/IGVFFI1089IXXN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/0a576ec6-4fbb-483b-8a45-8bc14f2fb8d6/IGVFFI1089IXXN.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-BioRep2-FFrep2-BinD-PCRrep1_S758_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6417LBMF/",
"accession": "IGVFFI6417LBMF",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-BinD-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T23:33:32.392990+00:00",
"file_format": "fastq",
"file_size": 3127793,
"href": "/sequence-files/IGVFFI6417LBMF/@@download/IGVFFI6417LBMF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/2ebe379c-f979-4ddf-a917-3d4b434b0223/IGVFFI6417LBMF.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-BioRep2-FFrep2-BinD-PCRrep1_S758_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3192YGUU/",
"accession": "IGVFFI3192YGUU",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-BinD-PCRrep4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T23:41:35.802782+00:00",
"file_format": "fastq",
"file_size": 7162140,
"href": "/sequence-files/IGVFFI3192YGUU/@@download/IGVFFI3192YGUU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/5ce98fc1-87b3-4c80-8b13-5ac8d6e082ae/IGVFFI3192YGUU.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-BioRep2-FFrep2-BinD-PCRrep4_S770_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/IGVFSM6449ZYML/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6449ZYML",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep2-FFrep2-BinD"
],
"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 76-100% 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": "2024-12-01T21:09:32.620772+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": "00ab6b69-b801-473e-b0a9-24f9301c6c2a"
}