{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1293ORGQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1293ORGQ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-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 [IGVFDS1293ORGQ](/measurement-sets/IGVFDS1293ORGQ/) 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/IGVFDS1293ORGQ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1293ORGQ](/measurement-sets/IGVFDS1293ORGQ/) has sequence file(s) [IGVFFI2259OCCH](/sequence-files/IGVFFI2259OCCH/), [IGVFFI0559FCUP](/sequence-files/IGVFFI0559FCUP/), [IGVFFI1635CQRI](/sequence-files/IGVFFI1635CQRI/), [IGVFFI2306OETW](/sequence-files/IGVFFI2306OETW/), [IGVFFI1620MDCN](/sequence-files/IGVFFI1620MDCN/), [IGVFFI7494YYGZ](/sequence-files/IGVFFI7494YYGZ/), [IGVFFI3898UZFY](/sequence-files/IGVFFI3898UZFY/), [IGVFFI5379RZFO](/sequence-files/IGVFFI5379RZFO/) 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/IGVFDS1293ORGQ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1293ORGQ](/measurement-sets/IGVFDS1293ORGQ/) has sequence file(s): [IGVFFI2259OCCH](/sequence-files/IGVFFI2259OCCH/), [IGVFFI0559FCUP](/sequence-files/IGVFFI0559FCUP/), [IGVFFI1635CQRI](/sequence-files/IGVFFI1635CQRI/), [IGVFFI2306OETW](/sequence-files/IGVFFI2306OETW/), [IGVFFI1620MDCN](/sequence-files/IGVFFI1620MDCN/), [IGVFFI7494YYGZ](/sequence-files/IGVFFI7494YYGZ/), [IGVFFI3898UZFY](/sequence-files/IGVFFI3898UZFY/), [IGVFFI5379RZFO](/sequence-files/IGVFFI5379RZFO/) 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/IGVFDS1293ORGQ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0994FYUT](/in-vitro-systems/IGVFSM0994FYUT/) 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/IGVFSM0994FYUT/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0994FYUT](/in-vitro-systems/IGVFSM0994FYUT/) 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/IGVFSM0994FYUT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing control for",
"detail": "Measurement set [IGVFDS1293ORGQ](/measurement-sets/IGVFDS1293ORGQ/) 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/IGVFDS1293ORGQ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1293ORGQ](/measurement-sets/IGVFDS1293ORGQ/) 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/IGVFDS1293ORGQ/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS1293ORGQ](/measurement-sets/IGVFDS1293ORGQ/) 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/IGVFDS1293ORGQ/"
}
]
},
"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": "2023-11-30T22:46:08.933074+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"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/IGVFFI2259OCCH/",
"accession": "IGVFFI2259OCCH",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:46:00.192749+00:00",
"file_format": "fastq",
"file_size": 73514447,
"href": "/sequence-files/IGVFFI2259OCCH/@@download/IGVFFI2259OCCH.fastq.gz",
"md5sum": "a2da524283b1074cf05d8e7acb4341bb",
"s3_uri": "s3://igvf-files/2023/12/05/81592433-b721-4280-a19e-6457d879520e/IGVFFI2259OCCH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-2-BinAll_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0559FCUP/",
"accession": "IGVFFI0559FCUP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:57:16.446390+00:00",
"file_format": "fastq",
"file_size": 14604274,
"href": "/sequence-files/IGVFFI0559FCUP/@@download/IGVFFI0559FCUP.fastq.gz",
"md5sum": "698032ecf169ab08a8e963016aa4d315",
"s3_uri": "s3://igvf-files/2023/12/05/132e7fae-d881-42cd-b403-76503b09fa05/IGVFFI0559FCUP.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-2-BinAll_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1635CQRI/",
"accession": "IGVFFI1635CQRI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:51:33.245612+00:00",
"file_format": "fastq",
"file_size": 16522180,
"href": "/sequence-files/IGVFFI1635CQRI/@@download/IGVFFI1635CQRI.fastq.gz",
"md5sum": "f9dde2d51ff79cb38d03f8e46f477490",
"s3_uri": "s3://igvf-files/2023/12/05/26cd4a0b-d66a-4ddc-83c9-f31f6e140da0/IGVFFI1635CQRI.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-1-BinAll_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2306OETW/",
"accession": "IGVFFI2306OETW",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:28:15.489815+00:00",
"file_format": "fastq",
"file_size": 44622399,
"href": "/sequence-files/IGVFFI2306OETW/@@download/IGVFFI2306OETW.fastq.gz",
"md5sum": "cdb28ef42262aa0a21839b1f75ad63bb",
"s3_uri": "s3://igvf-files/2023/12/05/fbc2bdf8-7ddf-437c-8cec-6160bf8ef227/IGVFFI2306OETW.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-1-BinAll_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1620MDCN/",
"accession": "IGVFFI1620MDCN",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:33:59.070281+00:00",
"file_format": "fastq",
"file_size": 40705102,
"href": "/sequence-files/IGVFFI1620MDCN/@@download/IGVFFI1620MDCN.fastq.gz",
"md5sum": "5cdd554077d5b57057c7880852afb73a",
"s3_uri": "s3://igvf-files/2023/12/05/4e2a7202-e357-4ba3-b005-ac06fe5cd6ed/IGVFFI1620MDCN.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-2-BinAll_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7494YYGZ/",
"accession": "IGVFFI7494YYGZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:39:58.228794+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI7494YYGZ/@@download/IGVFFI7494YYGZ.fastq.gz",
"md5sum": "9ed529d8a230fdd275348cca7513af4d",
"s3_uri": "s3://igvf-files/2023/12/05/6bebcf4e-1e32-44cf-a4f8-894415575ed8/IGVFFI7494YYGZ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
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"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-1-BinAll_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3898UZFY/",
"accession": "IGVFFI3898UZFY",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:02:48.381739+00:00",
"file_format": "fastq",
"file_size": 15019441,
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"md5sum": "b2bc3e32466fc2111f173e6f07a90f1d",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5379RZFO/",
"accession": "IGVFFI5379RZFO",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:08:23.105575+00:00",
"file_format": "fastq",
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"md5sum": "5cac3d27c8f662e301bf62ed7a073ce0",
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"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-6-D21-pPPIF-Amp-pPPIF-2-1-2-BinAll_I2_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": "2023-12-20T23:10:13.043845+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0994FYUT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0994FYUT",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-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": "2023-12-05T18:28:15.489815+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "22b438c6-5ad4-4433-8c62-cf76724bbc4b"
}