{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3899ANMJ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3899ANMJ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinF_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3899ANMJ](/measurement-sets/IGVFDS3899ANMJ/) has sequence file(s) [IGVFFI3862MRQM](/sequence-files/IGVFFI3862MRQM/), [IGVFFI8159VUGA](/sequence-files/IGVFFI8159VUGA/), [IGVFFI0228JWEI](/sequence-files/IGVFFI0228JWEI/), [IGVFFI5250EMTO](/sequence-files/IGVFFI5250EMTO/), [IGVFFI9391DBVT](/sequence-files/IGVFFI9391DBVT/), [IGVFFI6322RZLL](/sequence-files/IGVFFI6322RZLL/), [IGVFFI7426NBEW](/sequence-files/IGVFFI7426NBEW/), [IGVFFI3781WYKS](/sequence-files/IGVFFI3781WYKS/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS3899ANMJ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3899ANMJ](/measurement-sets/IGVFDS3899ANMJ/) has sequence file(s): [IGVFFI3862MRQM](/sequence-files/IGVFFI3862MRQM/), [IGVFFI8159VUGA](/sequence-files/IGVFFI8159VUGA/), [IGVFFI0228JWEI](/sequence-files/IGVFFI0228JWEI/), [IGVFFI5250EMTO](/sequence-files/IGVFFI5250EMTO/), [IGVFFI9391DBVT](/sequence-files/IGVFFI9391DBVT/), [IGVFFI6322RZLL](/sequence-files/IGVFFI6322RZLL/), [IGVFFI7426NBEW](/sequence-files/IGVFFI7426NBEW/), [IGVFFI3781WYKS](/sequence-files/IGVFFI3781WYKS/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS3899ANMJ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1757XEWZ](/in-vitro-systems/IGVFSM1757XEWZ/) 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/IGVFSM1757XEWZ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3899ANMJ](/measurement-sets/IGVFDS3899ANMJ/) 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/IGVFDS3899ANMJ/"
}
]
},
"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"
},
"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": [],
"creation_timestamp": "2023-11-30T22:46:41.045687+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/IGVFFI3862MRQM/",
"accession": "IGVFFI3862MRQM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinF-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:03:27.538267+00:00",
"file_format": "fastq",
"file_size": 2745556,
"href": "/sequence-files/IGVFFI3862MRQM/@@download/IGVFFI3862MRQM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/01518f48-1ffc-4b64-ae81-10fcbbf5ec29/IGVFFI3862MRQM.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-BioRep1-FFRep3-BinF-PCRrep2_S116_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8159VUGA/",
"accession": "IGVFFI8159VUGA",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinF-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:31:39.212353+00:00",
"file_format": "fastq",
"file_size": 7577463,
"href": "/sequence-files/IGVFFI8159VUGA/@@download/IGVFFI8159VUGA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c02fd944-4a69-4127-86d1-06019ea7af06/IGVFFI8159VUGA.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-BioRep1-FFRep3-BinF-PCRrep1_S20_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0228JWEI/",
"accession": "IGVFFI0228JWEI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinF-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:15:42.580432+00:00",
"file_format": "fastq",
"file_size": 2605444,
"href": "/sequence-files/IGVFFI0228JWEI/@@download/IGVFFI0228JWEI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/81a8fbd6-a897-4d72-9c3e-abe913c5ba6c/IGVFFI0228JWEI.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-BioRep1-FFRep3-BinF-PCRrep2_S116_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5250EMTO/",
"accession": "IGVFFI5250EMTO",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinF-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:37:54.743414+00:00",
"file_format": "fastq",
"file_size": 7513478,
"href": "/sequence-files/IGVFFI5250EMTO/@@download/IGVFFI5250EMTO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4afc4e9c-7f3a-4bb9-88f7-8efd605a8faa/IGVFFI5250EMTO.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-BioRep1-FFRep3-BinF-PCRrep2_S116_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9391DBVT/",
"accession": "IGVFFI9391DBVT",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinF-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:44:17.077294+00:00",
"file_format": "fastq",
"file_size": 14746373,
"href": "/sequence-files/IGVFFI9391DBVT/@@download/IGVFFI9391DBVT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/acb6cf4c-81af-4670-a8da-0f42aaa6fc87/IGVFFI9391DBVT.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-BioRep1-FFRep3-BinF-PCRrep1_S20_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6322RZLL/",
"accession": "IGVFFI6322RZLL",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinF-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:57:05.791211+00:00",
"file_format": "fastq",
"file_size": 2761304,
"href": "/sequence-files/IGVFFI6322RZLL/@@download/IGVFFI6322RZLL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f2b7aadd-d3b8-4d5f-b95d-11a215f8b1fa/IGVFFI6322RZLL.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-BioRep1-FFRep3-BinF-PCRrep1_S20_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7426NBEW/",
"accession": "IGVFFI7426NBEW",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinF-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:50:41.735011+00:00",
"file_format": "fastq",
"file_size": 15072545,
"href": "/sequence-files/IGVFFI7426NBEW/@@download/IGVFFI7426NBEW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c52a4e75-4459-4c8e-9d73-8918ec5f2c81/IGVFFI7426NBEW.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-BioRep1-FFRep3-BinF-PCRrep2_S116_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3781WYKS/",
"accession": "IGVFFI3781WYKS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinF-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:09:32.015137+00:00",
"file_format": "fastq",
"file_size": 2575813,
"href": "/sequence-files/IGVFFI3781WYKS/@@download/IGVFFI3781WYKS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/dd9445f9-758a-4142-a5ff-aa717b8cd23d/IGVFFI3781WYKS.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep1-FFRep3-BinF-PCRrep1_S20_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": "2023-12-20T23:10:40.887227+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1757XEWZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1757XEWZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinF"
],
"classifications": [
"cell line"
],
"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"
}
],
"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": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 90-100% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T18:31:39.212353+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"status": "released",
"symbol": "PPIF",
"synonyms": [
"rotamase F",
"CYP3",
"cyclophilin F",
"mitochondrial cyclophilin",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"CypD",
"Cyp-D",
"cyclophilin 3",
"cyclophilin D",
"CyP-M",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIase F"
]
}
],
"uuid": "fb676008-1191-4fbf-b590-6e868e8a197f"
}