{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3823MIDB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3823MIDB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-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": "mismatched status",
"detail": "Released in vitro system [IGVFSM7107DJSZ](/in-vitro-systems/IGVFSM7107DJSZ/) 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/IGVFSM7107DJSZ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7107DJSZ](/in-vitro-systems/IGVFSM7107DJSZ/) 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/IGVFSM7107DJSZ/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS3823MIDB](/measurement-sets/IGVFDS3823MIDB/) 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/IGVFDS3823MIDB/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3823MIDB](/measurement-sets/IGVFDS3823MIDB/) has sequence file(s) [IGVFFI7096BVAA](/sequence-files/IGVFFI7096BVAA/), [IGVFFI9225PMSN](/sequence-files/IGVFFI9225PMSN/), [IGVFFI4782IWQF](/sequence-files/IGVFFI4782IWQF/), [IGVFFI7020TLZR](/sequence-files/IGVFFI7020TLZR/), [IGVFFI7381DBUW](/sequence-files/IGVFFI7381DBUW/), [IGVFFI4489UIJT](/sequence-files/IGVFFI4489UIJT/), [IGVFFI9580IKXH](/sequence-files/IGVFFI9580IKXH/), [IGVFFI2449NFLL](/sequence-files/IGVFFI2449NFLL/) 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/IGVFDS3823MIDB/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3823MIDB](/measurement-sets/IGVFDS3823MIDB/) has sequence file(s): [IGVFFI7096BVAA](/sequence-files/IGVFFI7096BVAA/), [IGVFFI9225PMSN](/sequence-files/IGVFFI9225PMSN/), [IGVFFI4782IWQF](/sequence-files/IGVFFI4782IWQF/), [IGVFFI7020TLZR](/sequence-files/IGVFFI7020TLZR/), [IGVFFI7381DBUW](/sequence-files/IGVFFI7381DBUW/), [IGVFFI4489UIJT](/sequence-files/IGVFFI4489UIJT/), [IGVFFI9580IKXH](/sequence-files/IGVFFI9580IKXH/), [IGVFFI2449NFLL](/sequence-files/IGVFFI2449NFLL/) 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/IGVFDS3823MIDB/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing control for",
"detail": "Measurement set [IGVFDS3823MIDB](/measurement-sets/IGVFDS3823MIDB/) 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/IGVFDS3823MIDB/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3823MIDB](/measurement-sets/IGVFDS3823MIDB/) 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/IGVFDS3823MIDB/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS3823MIDB](/measurement-sets/IGVFDS3823MIDB/) 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/IGVFDS3823MIDB/"
}
]
},
"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": "2023-11-30T22:48:58.595053+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/IGVFFI7096BVAA/",
"accession": "IGVFFI7096BVAA",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:22:38.191373+00:00",
"file_format": "fastq",
"file_size": 922649,
"href": "/sequence-files/IGVFFI7096BVAA/@@download/IGVFFI7096BVAA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9012360a-53e8-4a5e-a6aa-b20ade4b4aeb/IGVFFI7096BVAA.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-FFrep3-BinAll-PCRrep2_S397_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9225PMSN/",
"accession": "IGVFFI9225PMSN",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:22:47.521441+00:00",
"file_format": "fastq",
"file_size": 3393237,
"href": "/sequence-files/IGVFFI9225PMSN/@@download/IGVFFI9225PMSN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a6ca0fa0-cd3b-43c5-a9ec-73757258e221/IGVFFI9225PMSN.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-FFrep3-BinAll-PCRrep2_S397_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4782IWQF/",
"accession": "IGVFFI4782IWQF",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:22:10.524746+00:00",
"file_format": "fastq",
"file_size": 3446052,
"href": "/sequence-files/IGVFFI4782IWQF/@@download/IGVFFI4782IWQF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c1b1795d-8201-44f8-9697-cb613146f020/IGVFFI4782IWQF.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-FFrep3-BinAll-PCRrep1_S387_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7020TLZR/",
"accession": "IGVFFI7020TLZR",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:21:52.383141+00:00",
"file_format": "fastq",
"file_size": 910665,
"href": "/sequence-files/IGVFFI7020TLZR/@@download/IGVFFI7020TLZR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e8251390-4589-46d5-a214-3e54becfde72/IGVFFI7020TLZR.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-FFrep3-BinAll-PCRrep1_S387_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7381DBUW/",
"accession": "IGVFFI7381DBUW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:22:28.942146+00:00",
"file_format": "fastq",
"file_size": 897977,
"href": "/sequence-files/IGVFFI7381DBUW/@@download/IGVFFI7381DBUW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6049937b-df6a-4f0e-8780-71f019b87378/IGVFFI7381DBUW.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-FFrep3-BinAll-PCRrep2_S397_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4489UIJT/",
"accession": "IGVFFI4489UIJT",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:22:56.990913+00:00",
"file_format": "fastq",
"file_size": 4031594,
"href": "/sequence-files/IGVFFI4489UIJT/@@download/IGVFFI4489UIJT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5c230a58-bb95-46c6-ace1-774182f857c2/IGVFFI4489UIJT.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-FFrep3-BinAll-PCRrep2_S397_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9580IKXH/",
"accession": "IGVFFI9580IKXH",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:22:01.472374+00:00",
"file_format": "fastq",
"file_size": 923643,
"href": "/sequence-files/IGVFFI9580IKXH/@@download/IGVFFI9580IKXH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/89f9c578-08ca-40fb-a985-85965f0bd805/IGVFFI9580IKXH.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-FFrep3-BinAll-PCRrep1_S387_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2449NFLL/",
"accession": "IGVFFI2449NFLL",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:22:19.682455+00:00",
"file_format": "fastq",
"file_size": 4095491,
"href": "/sequence-files/IGVFFI2449NFLL/@@download/IGVFFI2449NFLL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/34aab11b-3b70-43a1-bd8d-109241bb57e7/IGVFFI2449NFLL.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-FFrep3-BinAll-PCRrep1_S387_R2_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": "2023-12-20T23:05:44.213032+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7107DJSZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7107DJSZ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-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": "2023-12-05T20:21:52.383141+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "a03771eb-e2e2-427c-a3d4-e6de523b4a11"
}