{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0286JWIW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0286JWIW",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-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 [IGVFDS0286JWIW](/measurement-sets/IGVFDS0286JWIW/) 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/IGVFDS0286JWIW/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0286JWIW](/measurement-sets/IGVFDS0286JWIW/) has sequence file(s) [IGVFFI6356JMWU](/sequence-files/IGVFFI6356JMWU/), [IGVFFI4149BUYF](/sequence-files/IGVFFI4149BUYF/), [IGVFFI6592CNZV](/sequence-files/IGVFFI6592CNZV/), [IGVFFI9127KTTP](/sequence-files/IGVFFI9127KTTP/), [IGVFFI6704XSPG](/sequence-files/IGVFFI6704XSPG/), [IGVFFI8963OXEA](/sequence-files/IGVFFI8963OXEA/), [IGVFFI0192IEGC](/sequence-files/IGVFFI0192IEGC/), [IGVFFI0715ZDBC](/sequence-files/IGVFFI0715ZDBC/) 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/IGVFDS0286JWIW/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0286JWIW](/measurement-sets/IGVFDS0286JWIW/) has sequence file(s): [IGVFFI6356JMWU](/sequence-files/IGVFFI6356JMWU/), [IGVFFI4149BUYF](/sequence-files/IGVFFI4149BUYF/), [IGVFFI6592CNZV](/sequence-files/IGVFFI6592CNZV/), [IGVFFI9127KTTP](/sequence-files/IGVFFI9127KTTP/), [IGVFFI6704XSPG](/sequence-files/IGVFFI6704XSPG/), [IGVFFI8963OXEA](/sequence-files/IGVFFI8963OXEA/), [IGVFFI0192IEGC](/sequence-files/IGVFFI0192IEGC/), [IGVFFI0715ZDBC](/sequence-files/IGVFFI0715ZDBC/) 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/IGVFDS0286JWIW/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3814ESVL](/in-vitro-systems/IGVFSM3814ESVL/) has in progress subobject construct library set [IGVFDS6377KNCH](/construct-library-sets/IGVFDS6377KNCH/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM3814ESVL/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3814ESVL](/in-vitro-systems/IGVFSM3814ESVL/) 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/IGVFSM3814ESVL/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing control for",
"detail": "Measurement set [IGVFDS0286JWIW](/measurement-sets/IGVFDS0286JWIW/) 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/IGVFDS0286JWIW/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0286JWIW](/measurement-sets/IGVFDS0286JWIW/) 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/IGVFDS0286JWIW/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS0286JWIW](/measurement-sets/IGVFDS0286JWIW/) 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/IGVFDS0286JWIW/"
}
]
},
"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/IGVFDS6377KNCH/",
"accession": "IGVFDS6377KNCH",
"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/IGVFDS6385JXFZ/",
"accession": "IGVFDS6385JXFZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-THP1-PE2_Exp3_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"control_type": "unsorted FACS input",
"creation_timestamp": "2023-11-30T22:46:54.578200+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/IGVFFI6356JMWU/",
"accession": "IGVFFI6356JMWU",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep3-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:34:56.159920+00:00",
"file_format": "fastq",
"file_size": 8239681,
"href": "/sequence-files/IGVFFI6356JMWU/@@download/IGVFFI6356JMWU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8c93b5d3-165a-432e-a7a1-e617635b3260/IGVFFI6356JMWU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep3-BinAll-PCRrep1_S42_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4149BUYF/",
"accession": "IGVFFI4149BUYF",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep3-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:00:26.233506+00:00",
"file_format": "fastq",
"file_size": 2765662,
"href": "/sequence-files/IGVFFI4149BUYF/@@download/IGVFFI4149BUYF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/99712e6c-6302-4fc6-94be-c493bb7eae62/IGVFFI4149BUYF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep3-BinAll-PCRrep1_S42_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6592CNZV/",
"accession": "IGVFFI6592CNZV",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep3-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:06:38.602087+00:00",
"file_format": "fastq",
"file_size": 2937704,
"href": "/sequence-files/IGVFFI6592CNZV/@@download/IGVFFI6592CNZV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/afe411ba-8952-41ce-8531-901583d27161/IGVFFI6592CNZV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep3-BinAll-PCRrep2_S138_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9127KTTP/",
"accession": "IGVFFI9127KTTP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep3-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:54:10.170833+00:00",
"file_format": "fastq",
"file_size": 17741327,
"href": "/sequence-files/IGVFFI9127KTTP/@@download/IGVFFI9127KTTP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8f7c7b0d-4bce-41e9-9e90-a5da459547b7/IGVFFI9127KTTP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep3-BinAll-PCRrep2_S138_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6704XSPG/",
"accession": "IGVFFI6704XSPG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep3-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:18:58.619674+00:00",
"file_format": "fastq",
"file_size": 2900925,
"href": "/sequence-files/IGVFFI6704XSPG/@@download/IGVFFI6704XSPG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a5f5c346-64c0-4fc0-aa3c-0be3cce432f7/IGVFFI6704XSPG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep3-BinAll-PCRrep2_S138_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8963OXEA/",
"accession": "IGVFFI8963OXEA",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep3-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:41:13.628830+00:00",
"file_format": "fastq",
"file_size": 8696379,
"href": "/sequence-files/IGVFFI8963OXEA/@@download/IGVFFI8963OXEA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/623276d5-1c73-4228-996c-08e37b4fc6fe/IGVFFI8963OXEA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep3-BinAll-PCRrep2_S138_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0192IEGC/",
"accession": "IGVFFI0192IEGC",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep3-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:12:47.916518+00:00",
"file_format": "fastq",
"file_size": 2706239,
"href": "/sequence-files/IGVFFI0192IEGC/@@download/IGVFFI0192IEGC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3740cd1d-8ae7-400b-a223-78323c372479/IGVFFI0192IEGC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep3-BinAll-PCRrep1_S42_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0715ZDBC/",
"accession": "IGVFFI0715ZDBC",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep3-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:47:38.551656+00:00",
"file_format": "fastq",
"file_size": 15901251,
"href": "/sequence-files/IGVFFI0715ZDBC/@@download/IGVFFI0715ZDBC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/104954d3-3855-4c44-8523-6ac0248929bf/IGVFFI0715ZDBC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep3-BinAll-PCRrep1_S42_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5056OAGR/"
],
"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": "2023-12-20T23:10:44.609080+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3814ESVL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3814ESVL",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-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": "2023-12-05T18:34:56.159920+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "3fa371ec-7030-4eb5-81ca-9340e34bdb38"
}