{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4736IKQS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4736IKQS",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0906STHP](/in-vitro-systems/IGVFSM0906STHP/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM0906STHP/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4736IKQS](/measurement-sets/IGVFDS4736IKQS/) has sequence file(s) [IGVFFI2514XTTV](/sequence-files/IGVFFI2514XTTV/), [IGVFFI3816VGNF](/sequence-files/IGVFFI3816VGNF/), [IGVFFI0289RFIQ](/sequence-files/IGVFFI0289RFIQ/), [IGVFFI4860HGYN](/sequence-files/IGVFFI4860HGYN/), [IGVFFI7195UIPO](/sequence-files/IGVFFI7195UIPO/), [IGVFFI5148OFCU](/sequence-files/IGVFFI5148OFCU/), [IGVFFI3621TWXC](/sequence-files/IGVFFI3621TWXC/), [IGVFFI2898XJUM](/sequence-files/IGVFFI2898XJUM/) 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/IGVFDS4736IKQS/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4736IKQS](/measurement-sets/IGVFDS4736IKQS/) has sequence file(s): [IGVFFI2514XTTV](/sequence-files/IGVFFI2514XTTV/), [IGVFFI3816VGNF](/sequence-files/IGVFFI3816VGNF/), [IGVFFI0289RFIQ](/sequence-files/IGVFFI0289RFIQ/), [IGVFFI4860HGYN](/sequence-files/IGVFFI4860HGYN/), [IGVFFI7195UIPO](/sequence-files/IGVFFI7195UIPO/), [IGVFFI5148OFCU](/sequence-files/IGVFFI5148OFCU/), [IGVFFI3621TWXC](/sequence-files/IGVFFI3621TWXC/), [IGVFFI2898XJUM](/sequence-files/IGVFFI2898XJUM/) 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/IGVFDS4736IKQS/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4736IKQS](/measurement-sets/IGVFDS4736IKQS/) 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/IGVFDS4736IKQS/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS4736IKQS](/measurement-sets/IGVFDS4736IKQS/) has no `targeted_genes`. ChIP-seq and CRISPR flow cytometry assays are expected to specify targeted gene(s).",
"level": 40,
"level_name": "WARNING",
"name": "audit_targeted_genes",
"path": "/measurement-sets/IGVFDS4736IKQS/"
}
]
},
"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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"control_type": "unsorted FACS input",
"creation_timestamp": "2023-11-30T22:49:25.539684+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/IGVFFI2514XTTV/",
"accession": "IGVFFI2514XTTV",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:31:25.114899+00:00",
"file_format": "fastq",
"file_size": 962467,
"href": "/sequence-files/IGVFFI2514XTTV/@@download/IGVFFI2514XTTV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3a9e847c-e02e-4759-8888-9475d315df32/IGVFFI2514XTTV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinAll-PCRrep2_S402_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3816VGNF/",
"accession": "IGVFFI3816VGNF",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:31:06.424608+00:00",
"file_format": "fastq",
"file_size": 4260671,
"href": "/sequence-files/IGVFFI3816VGNF/@@download/IGVFFI3816VGNF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/20f83b68-1bab-4478-81a6-6fe4baebbdc0/IGVFFI3816VGNF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinAll-PCRrep1_S392_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0289RFIQ/",
"accession": "IGVFFI0289RFIQ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:30:57.185252+00:00",
"file_format": "fastq",
"file_size": 3595175,
"href": "/sequence-files/IGVFFI0289RFIQ/@@download/IGVFFI0289RFIQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/51a451c6-bd4a-4a48-be2c-09a88481e851/IGVFFI0289RFIQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinAll-PCRrep1_S392_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4860HGYN/",
"accession": "IGVFFI4860HGYN",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:31:43.599138+00:00",
"file_format": "fastq",
"file_size": 4214023,
"href": "/sequence-files/IGVFFI4860HGYN/@@download/IGVFFI4860HGYN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2d6db900-8d1d-4670-9ba8-0c46ddd99280/IGVFFI4860HGYN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinAll-PCRrep2_S402_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7195UIPO/",
"accession": "IGVFFI7195UIPO",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:30:48.163087+00:00",
"file_format": "fastq",
"file_size": 964003,
"href": "/sequence-files/IGVFFI7195UIPO/@@download/IGVFFI7195UIPO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/130fb8fa-10ad-415f-8dfe-f5f4a3562c17/IGVFFI7195UIPO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinAll-PCRrep1_S392_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5148OFCU/",
"accession": "IGVFFI5148OFCU",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:31:34.248072+00:00",
"file_format": "fastq",
"file_size": 3543215,
"href": "/sequence-files/IGVFFI5148OFCU/@@download/IGVFFI5148OFCU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/347648bc-fd1d-4ea3-a249-1f83f3c865cc/IGVFFI5148OFCU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinAll-PCRrep2_S402_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3621TWXC/",
"accession": "IGVFFI3621TWXC",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:31:15.852886+00:00",
"file_format": "fastq",
"file_size": 1025051,
"href": "/sequence-files/IGVFFI3621TWXC/@@download/IGVFFI3621TWXC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7b9f2053-d9a5-4e3e-ab1d-6828c8a61cda/IGVFFI3621TWXC.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinAll-PCRrep2_S402_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2898XJUM/",
"accession": "IGVFFI2898XJUM",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:30:38.677982+00:00",
"file_format": "fastq",
"file_size": 1026530,
"href": "/sequence-files/IGVFFI2898XJUM/@@download/IGVFFI2898XJUM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/23a87139-2921-42b0-9f45-0891a6241930/IGVFFI2898XJUM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-BinAll-PCRrep1_S392_I1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5031MNRR/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set. 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"
],
"release_timestamp": "2023-12-20T23:05:40.132076+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0906STHP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0906STHP",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2374NXLW/",
"accession": "IGVFDS2374NXLW",
"file_set_type": "guide library",
"status": "in progress",
"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": "released",
"summary": "THP-1 cell line, male, Homo sapiens modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T23:30:38.677982+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "fe6d143f-dbd2-40a5-b72b-55021f81951f"
}