{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2963KTVM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2963KTVM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinF_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 [IGVFDS2963KTVM](/measurement-sets/IGVFDS2963KTVM/) 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/IGVFDS2963KTVM/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2963KTVM](/measurement-sets/IGVFDS2963KTVM/) has sequence file(s) [IGVFFI8714LLSC](/sequence-files/IGVFFI8714LLSC/), [IGVFFI5349DVDP](/sequence-files/IGVFFI5349DVDP/), [IGVFFI8142YGKR](/sequence-files/IGVFFI8142YGKR/), [IGVFFI9287ZVPJ](/sequence-files/IGVFFI9287ZVPJ/), [IGVFFI9094MNSW](/sequence-files/IGVFFI9094MNSW/), [IGVFFI4943VYFO](/sequence-files/IGVFFI4943VYFO/), [IGVFFI3085OIOQ](/sequence-files/IGVFFI3085OIOQ/), [IGVFFI8147USKG](/sequence-files/IGVFFI8147USKG/) 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/IGVFDS2963KTVM/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2963KTVM](/measurement-sets/IGVFDS2963KTVM/) has sequence file(s): [IGVFFI8714LLSC](/sequence-files/IGVFFI8714LLSC/), [IGVFFI5349DVDP](/sequence-files/IGVFFI5349DVDP/), [IGVFFI8142YGKR](/sequence-files/IGVFFI8142YGKR/), [IGVFFI9287ZVPJ](/sequence-files/IGVFFI9287ZVPJ/), [IGVFFI9094MNSW](/sequence-files/IGVFFI9094MNSW/), [IGVFFI4943VYFO](/sequence-files/IGVFFI4943VYFO/), [IGVFFI3085OIOQ](/sequence-files/IGVFFI3085OIOQ/), [IGVFFI8147USKG](/sequence-files/IGVFFI8147USKG/) 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/IGVFDS2963KTVM/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1400DZMP](/in-vitro-systems/IGVFSM1400DZMP/) 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/IGVFSM1400DZMP/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1400DZMP](/in-vitro-systems/IGVFSM1400DZMP/) 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/IGVFSM1400DZMP/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2963KTVM](/measurement-sets/IGVFDS2963KTVM/) 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/IGVFDS2963KTVM/"
}
]
},
"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": [],
"creation_timestamp": "2023-11-30T22:46:28.774105+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/IGVFFI8714LLSC/",
"accession": "IGVFFI8714LLSC",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:13:40.102667+00:00",
"file_format": "fastq",
"file_size": 2822273,
"href": "/sequence-files/IGVFFI8714LLSC/@@download/IGVFFI8714LLSC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9232015b-d768-4771-a776-6085e6e955e9/IGVFFI8714LLSC.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-FFRep1-BinF-PCRrep2_S102_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5349DVDP/",
"accession": "IGVFFI5349DVDP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:35:49.332373+00:00",
"file_format": "fastq",
"file_size": 8115741,
"href": "/sequence-files/IGVFFI5349DVDP/@@download/IGVFFI5349DVDP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c79f55e8-b90d-4f98-a1cf-346624c3f0a6/IGVFFI5349DVDP.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-FFRep1-BinF-PCRrep2_S102_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8142YGKR/",
"accession": "IGVFFI8142YGKR",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:42:08.522444+00:00",
"file_format": "fastq",
"file_size": 16198606,
"href": "/sequence-files/IGVFFI8142YGKR/@@download/IGVFFI8142YGKR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/37ef5cda-d0f2-45a0-8935-48498cddd3dd/IGVFFI8142YGKR.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-FFRep1-BinF-PCRrep1_S6_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9287ZVPJ/",
"accession": "IGVFFI9287ZVPJ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:07:30.378005+00:00",
"file_format": "fastq",
"file_size": 2783668,
"href": "/sequence-files/IGVFFI9287ZVPJ/@@download/IGVFFI9287ZVPJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0f03d076-a3b9-414d-9d93-5bae34eda31b/IGVFFI9287ZVPJ.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-FFRep1-BinF-PCRrep1_S6_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9094MNSW/",
"accession": "IGVFFI9094MNSW",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:01:22.677997+00:00",
"file_format": "fastq",
"file_size": 2870957,
"href": "/sequence-files/IGVFFI9094MNSW/@@download/IGVFFI9094MNSW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c1f920ce-df65-4dc1-beee-b5dd2eaa7716/IGVFFI9094MNSW.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-FFRep1-BinF-PCRrep2_S102_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4943VYFO/",
"accession": "IGVFFI4943VYFO",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:29:29.795706+00:00",
"file_format": "fastq",
"file_size": 8166926,
"href": "/sequence-files/IGVFFI4943VYFO/@@download/IGVFFI4943VYFO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b4f414cf-0e04-473d-b4f6-a12c110b1325/IGVFFI4943VYFO.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-FFRep1-BinF-PCRrep1_S6_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3085OIOQ/",
"accession": "IGVFFI3085OIOQ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:48:33.368988+00:00",
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"file_size": 16721699,
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"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-FFRep1-BinF-PCRrep2_S102_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8147USKG/",
"accession": "IGVFFI8147USKG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinF-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:55:02.898987+00:00",
"file_format": "fastq",
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"s3_uri": "s3://igvf-files/2023/12/05/9d39515d-37e9-4eed-84ac-bc10212a7cee/IGVFFI8147USKG.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-FFRep1-BinF-PCRrep1_S6_I1_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": "2023-12-20T23:10:20.665205+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1400DZMP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1400DZMP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-BinF"
],
"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 (sorting details: FACS bin for 90-100% expression of PPIF) 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": "2023-12-05T18:29:29.795706+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF 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": [
"PPIase F",
"peptidylprolyl isomerase F",
"Cyp-D",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIF",
"CyP-M",
"cyclophilin F",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"cyclophilin 3",
"cyclophilin D",
"rotamase F",
"mitochondrial cyclophilin",
"CypD",
"CYP3"
]
}
],
"uuid": "e6029737-b559-44bb-ba4c-93e467e7f234"
}