{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8050CYYG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8050CYYG",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8050CYYG](/measurement-sets/IGVFDS8050CYYG/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/measurement-sets/IGVFDS8050CYYG/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8050CYYG](/measurement-sets/IGVFDS8050CYYG/) has sequence file(s) [IGVFFI9547HEZD](/sequence-files/IGVFFI9547HEZD/), [IGVFFI3649JAGF](/sequence-files/IGVFFI3649JAGF/), [IGVFFI4700NWVO](/sequence-files/IGVFFI4700NWVO/), [IGVFFI6145UWTR](/sequence-files/IGVFFI6145UWTR/), [IGVFFI3805VYAH](/sequence-files/IGVFFI3805VYAH/), [IGVFFI5505ATDV](/sequence-files/IGVFFI5505ATDV/), [IGVFFI4338UVFK](/sequence-files/IGVFFI4338UVFK/), [IGVFFI0896THZT](/sequence-files/IGVFFI0896THZT/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS8050CYYG/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8050CYYG](/measurement-sets/IGVFDS8050CYYG/) has sequence file(s): [IGVFFI9547HEZD](/sequence-files/IGVFFI9547HEZD/), [IGVFFI3649JAGF](/sequence-files/IGVFFI3649JAGF/), [IGVFFI4700NWVO](/sequence-files/IGVFFI4700NWVO/), [IGVFFI6145UWTR](/sequence-files/IGVFFI6145UWTR/), [IGVFFI3805VYAH](/sequence-files/IGVFFI3805VYAH/), [IGVFFI5505ATDV](/sequence-files/IGVFFI5505ATDV/), [IGVFFI4338UVFK](/sequence-files/IGVFFI4338UVFK/), [IGVFFI0896THZT](/sequence-files/IGVFFI0896THZT/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS8050CYYG/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5729BNQM](/in-vitro-systems/IGVFSM5729BNQM/) 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/IGVFSM5729BNQM/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM5729BNQM](/in-vitro-systems/IGVFSM5729BNQM/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/in-vitro-systems/IGVFSM5729BNQM/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing control for",
"detail": "Measurement set [IGVFDS8050CYYG](/measurement-sets/IGVFDS8050CYYG/) has no `control_for`. The `control_file_sets` should be patched on the file sets it serves as a control for and this property, `control_for`, will be reverse calculated. File sets that specify a control type are expected to be a control for other file sets.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_control_for_control_type",
"path": "/measurement-sets/IGVFDS8050CYYG/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8050CYYG](/measurement-sets/IGVFDS8050CYYG/) 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/IGVFDS8050CYYG/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS8050CYYG](/measurement-sets/IGVFDS8050CYYG/) 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/IGVFDS8050CYYG/"
}
]
},
"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"
},
"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"
}
],
"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": "2023-11-30T22:49:19.551308+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/IGVFFI9547HEZD/",
"accession": "IGVFFI9547HEZD",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:00:07.171080+00:00",
"file_format": "fastq",
"file_size": 3948089,
"href": "/sequence-files/IGVFFI9547HEZD/@@download/IGVFFI9547HEZD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4d2249a7-cd70-4acc-b881-7e63eb73f168/IGVFFI9547HEZD.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-FFrep3-BinAll-PCRrep1_S391_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3649JAGF/",
"accession": "IGVFFI3649JAGF",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:59:39.301619+00:00",
"file_format": "fastq",
"file_size": 927703,
"href": "/sequence-files/IGVFFI3649JAGF/@@download/IGVFFI3649JAGF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5d9b0fd6-df2c-4d4a-98f9-c15c8649484b/IGVFFI3649JAGF.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-FFrep3-BinAll-PCRrep1_S391_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4700NWVO/",
"accession": "IGVFFI4700NWVO",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:00:25.661417+00:00",
"file_format": "fastq",
"file_size": 958509,
"href": "/sequence-files/IGVFFI4700NWVO/@@download/IGVFFI4700NWVO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e6db6218-d83d-4587-a0fc-66e24d1b57a6/IGVFFI4700NWVO.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-FFrep3-BinAll-PCRrep2_S401_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6145UWTR/",
"accession": "IGVFFI6145UWTR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:59:48.432569+00:00",
"file_format": "fastq",
"file_size": 892072,
"href": "/sequence-files/IGVFFI6145UWTR/@@download/IGVFFI6145UWTR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7003507e-8840-4943-919f-41ec85f49f7f/IGVFFI6145UWTR.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-FFrep3-BinAll-PCRrep1_S391_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3805VYAH/",
"accession": "IGVFFI3805VYAH",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:00:44.402624+00:00",
"file_format": "fastq",
"file_size": 4180049,
"href": "/sequence-files/IGVFFI3805VYAH/@@download/IGVFFI3805VYAH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fd62c100-35b2-470d-810f-b5f9d9bcdb9d/IGVFFI3805VYAH.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-FFrep3-BinAll-PCRrep2_S401_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5505ATDV/",
"accession": "IGVFFI5505ATDV",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:00:35.128209+00:00",
"file_format": "fastq",
"file_size": 3543027,
"href": "/sequence-files/IGVFFI5505ATDV/@@download/IGVFFI5505ATDV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8af371af-839e-4593-a614-920641056b31/IGVFFI5505ATDV.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-FFrep3-BinAll-PCRrep2_S401_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4338UVFK/",
"accession": "IGVFFI4338UVFK",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:59:57.659585+00:00",
"file_format": "fastq",
"file_size": 3315735,
"href": "/sequence-files/IGVFFI4338UVFK/@@download/IGVFFI4338UVFK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/238160c5-f1a8-4528-b3c7-2e8bcb5110e8/IGVFFI4338UVFK.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-FFrep3-BinAll-PCRrep1_S391_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0896THZT/",
"accession": "IGVFFI0896THZT",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T23:00:16.612905+00:00",
"file_format": "fastq",
"file_size": 959587,
"href": "/sequence-files/IGVFFI0896THZT/@@download/IGVFFI0896THZT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/79ef3559-c540-4232-a7c6-b3c64551930b/IGVFFI0896THZT.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-FFrep3-BinAll-PCRrep2_S401_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": "2023-12-20T23:05:27.649195+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5729BNQM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5729BNQM",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep3-FACS_Input"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"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": "Homo sapiens (male) THP-1 cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T22:59:39.301619+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "64287c71-9d52-4166-88c5-443471305779"
}