{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5892ADAN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5892ADAN",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-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 [IGVFDS5892ADAN](/measurement-sets/IGVFDS5892ADAN/) 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/IGVFDS5892ADAN/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5892ADAN](/measurement-sets/IGVFDS5892ADAN/) has sequence file(s) [IGVFFI0273PXXR](/sequence-files/IGVFFI0273PXXR/), [IGVFFI0272YVFR](/sequence-files/IGVFFI0272YVFR/), [IGVFFI0833RQPW](/sequence-files/IGVFFI0833RQPW/), [IGVFFI6009HGRM](/sequence-files/IGVFFI6009HGRM/), [IGVFFI7524SQKQ](/sequence-files/IGVFFI7524SQKQ/), [IGVFFI8854WVRI](/sequence-files/IGVFFI8854WVRI/), [IGVFFI4489JCVF](/sequence-files/IGVFFI4489JCVF/), [IGVFFI2237YQSP](/sequence-files/IGVFFI2237YQSP/) 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/IGVFDS5892ADAN/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5892ADAN](/measurement-sets/IGVFDS5892ADAN/) has sequence file(s): [IGVFFI0273PXXR](/sequence-files/IGVFFI0273PXXR/), [IGVFFI0272YVFR](/sequence-files/IGVFFI0272YVFR/), [IGVFFI0833RQPW](/sequence-files/IGVFFI0833RQPW/), [IGVFFI6009HGRM](/sequence-files/IGVFFI6009HGRM/), [IGVFFI7524SQKQ](/sequence-files/IGVFFI7524SQKQ/), [IGVFFI8854WVRI](/sequence-files/IGVFFI8854WVRI/), [IGVFFI4489JCVF](/sequence-files/IGVFFI4489JCVF/), [IGVFFI2237YQSP](/sequence-files/IGVFFI2237YQSP/) 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/IGVFDS5892ADAN/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5918TEKW](/in-vitro-systems/IGVFSM5918TEKW/) 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/IGVFSM5918TEKW/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM5918TEKW](/in-vitro-systems/IGVFSM5918TEKW/) 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/IGVFSM5918TEKW/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing control for",
"detail": "Measurement set [IGVFDS5892ADAN](/measurement-sets/IGVFDS5892ADAN/) 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/IGVFDS5892ADAN/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5892ADAN](/measurement-sets/IGVFDS5892ADAN/) 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/IGVFDS5892ADAN/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS5892ADAN](/measurement-sets/IGVFDS5892ADAN/) 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/IGVFDS5892ADAN/"
}
]
},
"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": "2023-11-30T22:49:03.645560+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/IGVFFI0273PXXR/",
"accession": "IGVFFI0273PXXR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:53:12.200273+00:00",
"file_format": "fastq",
"file_size": 3569796,
"href": "/sequence-files/IGVFFI0273PXXR/@@download/IGVFFI0273PXXR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c6165dd3-5cd4-45ed-be95-7cebd7b44dca/IGVFFI0273PXXR.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-BioRep1-FFrep4-BinAll-PCRrep1_S388_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0272YVFR/",
"accession": "IGVFFI0272YVFR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:53:49.016294+00:00",
"file_format": "fastq",
"file_size": 3505951,
"href": "/sequence-files/IGVFFI0272YVFR/@@download/IGVFFI0272YVFR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b59bda51-839b-49e2-ba67-e5565b1017e7/IGVFFI0272YVFR.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-BioRep1-FFrep4-BinAll-PCRrep2_S398_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0833RQPW/",
"accession": "IGVFFI0833RQPW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:53:02.995332+00:00",
"file_format": "fastq",
"file_size": 950753,
"href": "/sequence-files/IGVFFI0833RQPW/@@download/IGVFFI0833RQPW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/78dcc094-26d9-46c7-8311-86e24c8a2023/IGVFFI0833RQPW.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-BioRep1-FFrep4-BinAll-PCRrep1_S388_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6009HGRM/",
"accession": "IGVFFI6009HGRM",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:53:21.491032+00:00",
"file_format": "fastq",
"file_size": 4198494,
"href": "/sequence-files/IGVFFI6009HGRM/@@download/IGVFFI6009HGRM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/419220bd-937c-45d4-bfb6-ff5246c08fd7/IGVFFI6009HGRM.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-BioRep1-FFrep4-BinAll-PCRrep1_S388_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7524SQKQ/",
"accession": "IGVFFI7524SQKQ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:53:30.786638+00:00",
"file_format": "fastq",
"file_size": 961013,
"href": "/sequence-files/IGVFFI7524SQKQ/@@download/IGVFFI7524SQKQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d1e8e25d-ffb4-44f1-bfee-74b33959cdcb/IGVFFI7524SQKQ.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-BioRep1-FFrep4-BinAll-PCRrep2_S398_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8854WVRI/",
"accession": "IGVFFI8854WVRI",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:53:39.966002+00:00",
"file_format": "fastq",
"file_size": 942750,
"href": "/sequence-files/IGVFFI8854WVRI/@@download/IGVFFI8854WVRI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8260deef-f50c-4820-bab6-0aea8e710f4f/IGVFFI8854WVRI.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-BioRep1-FFrep4-BinAll-PCRrep2_S398_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4489JCVF/",
"accession": "IGVFFI4489JCVF",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:53:58.384237+00:00",
"file_format": "fastq",
"file_size": 4148555,
"href": "/sequence-files/IGVFFI4489JCVF/@@download/IGVFFI4489JCVF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d1145390-f785-446b-9298-7500d7a327cd/IGVFFI4489JCVF.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-BioRep1-FFrep4-BinAll-PCRrep2_S398_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2237YQSP/",
"accession": "IGVFFI2237YQSP",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:52:53.760296+00:00",
"file_format": "fastq",
"file_size": 995815,
"href": "/sequence-files/IGVFFI2237YQSP/@@download/IGVFFI2237YQSP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b880f415-366e-4e27-862c-951c94f83d04/IGVFFI2237YQSP.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-BioRep1-FFrep4-BinAll-PCRrep1_S388_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": "2023-12-20T23:05:35.732913+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5918TEKW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5918TEKW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep4-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": "2023-12-05T20:52:53.760296+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "6e5f92e3-4159-43f5-864c-4f8be161116c"
}