{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6884MESW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6884MESW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003133/",
"term_name": "cas mediated mutagenesis"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM7935BTPN](/in-vitro-systems/IGVFSM7935BTPN/) 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/IGVFSM7935BTPN/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6884MESW](/measurement-sets/IGVFDS6884MESW/) has sequence file(s): [IGVFFI8006YZRM](/sequence-files/IGVFFI8006YZRM/), [IGVFFI5655NKLE](/sequence-files/IGVFFI5655NKLE/), [IGVFFI2316STRE](/sequence-files/IGVFFI2316STRE/), [IGVFFI3326JQOC](/sequence-files/IGVFFI3326JQOC/), [IGVFFI1219VFUN](/sequence-files/IGVFFI1219VFUN/), [IGVFFI8365HPGR](/sequence-files/IGVFFI8365HPGR/), [IGVFFI0717LTHJ](/sequence-files/IGVFFI0717LTHJ/), [IGVFFI5749XIDR](/sequence-files/IGVFFI5749XIDR/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS6884MESW/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6884MESW](/measurement-sets/IGVFDS6884MESW/) 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": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_CRISPR_assay_missing_cell_sorting_auxiliary_set",
"path": "/measurement-sets/IGVFDS6884MESW/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6884MESW](/measurement-sets/IGVFDS6884MESW/) has no variant sequencing `auxiliary_sets`. Variant FlowFISH measurement sets are expected to link to a variant sequencing auxiliary set.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_Variant_FlowFISH_missing_variant_sequencing_auxiliary_set",
"path": "/measurement-sets/IGVFDS6884MESW/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS6884MESW](/measurement-sets/IGVFDS6884MESW/) has no `targeted_genes`. ChIP-seq and FISH-based assays are expected to specify targeted gene(s).",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_targeted_genes",
"path": "/measurement-sets/IGVFDS6884MESW/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6884MESW](/measurement-sets/IGVFDS6884MESW/) has sequence file(s) [IGVFFI8006YZRM](/sequence-files/IGVFFI8006YZRM/), [IGVFFI5655NKLE](/sequence-files/IGVFFI5655NKLE/), [IGVFFI2316STRE](/sequence-files/IGVFFI2316STRE/), [IGVFFI3326JQOC](/sequence-files/IGVFFI3326JQOC/), [IGVFFI1219VFUN](/sequence-files/IGVFFI1219VFUN/), [IGVFFI8365HPGR](/sequence-files/IGVFFI8365HPGR/), [IGVFFI0717LTHJ](/sequence-files/IGVFFI0717LTHJ/), [IGVFFI5749XIDR](/sequence-files/IGVFFI5749XIDR/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS6884MESW/"
}
]
},
"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/IGVFDS9477ARWI/",
"accession": "IGVFDS9477ARWI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing",
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:48:20.144980+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI8006YZRM/",
"accession": "IGVFFI8006YZRM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep1_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T19:35:13.422866+00:00",
"file_format": "fastq",
"file_size": 7542054,
"href": "/sequence-files/IGVFFI8006YZRM/@@download/IGVFFI8006YZRM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/340f6159-454e-4ef4-856d-c3a9fe783f40/IGVFFI8006YZRM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinC-PCRrep1_S143_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5655NKLE/",
"accession": "IGVFFI5655NKLE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep1_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T19:43:39.248777+00:00",
"file_format": "fastq",
"file_size": 13969061,
"href": "/sequence-files/IGVFFI5655NKLE/@@download/IGVFFI5655NKLE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f6109d67-0c85-46d8-8dec-cd9332de92d8/IGVFFI5655NKLE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinC-PCRrep1_S143_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2316STRE/",
"accession": "IGVFFI2316STRE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep1_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T19:52:04.471219+00:00",
"file_format": "fastq",
"file_size": 3242107,
"href": "/sequence-files/IGVFFI2316STRE/@@download/IGVFFI2316STRE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ba7e896a-3185-457f-88b8-a3ac549144d0/IGVFFI2316STRE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinC-PCRrep1_S143_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3326JQOC/",
"accession": "IGVFFI3326JQOC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep1_I2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:00:11.640252+00:00",
"file_format": "fastq",
"file_size": 3158646,
"href": "/sequence-files/IGVFFI3326JQOC/@@download/IGVFFI3326JQOC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/29547d3c-2194-4a58-b783-143486433da3/IGVFFI3326JQOC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinC-PCRrep1_S143_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1219VFUN/",
"accession": "IGVFFI1219VFUN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep2_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:08:24.744430+00:00",
"file_format": "fastq",
"file_size": 7354088,
"href": "/sequence-files/IGVFFI1219VFUN/@@download/IGVFFI1219VFUN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/616e90f7-dea8-4762-82eb-cef86baef465/IGVFFI1219VFUN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinC-PCRrep2_S200_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8365HPGR/",
"accession": "IGVFFI8365HPGR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep2_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:16:50.613869+00:00",
"file_format": "fastq",
"file_size": 13570142,
"href": "/sequence-files/IGVFFI8365HPGR/@@download/IGVFFI8365HPGR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/87c0c115-fbff-42b7-a051-aafe50bd493b/IGVFFI8365HPGR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinC-PCRrep2_S200_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0717LTHJ/",
"accession": "IGVFFI0717LTHJ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep2_I2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:33:30.655770+00:00",
"file_format": "fastq",
"file_size": 3080263,
"href": "/sequence-files/IGVFFI0717LTHJ/@@download/IGVFFI0717LTHJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0422e4e2-e136-456b-8184-8ab9bdd51599/IGVFFI0717LTHJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinC-PCRrep2_S200_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5749XIDR/",
"accession": "IGVFFI5749XIDR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC-PCRrep2_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-05T20:25:17.464997+00:00",
"file_format": "fastq",
"file_size": 3159483,
"href": "/sequence-files/IGVFFI5749XIDR/@@download/IGVFFI5749XIDR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4e5a68c1-1c2b-4556-ad00-53b41f9464ea/IGVFFI5749XIDR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinC-PCRrep2_S200_I1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_file_set_for": [
"/analysis-sets/IGVFDS1863TJOE/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "Variant FlowFISH",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:05:13.034937+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7935BTPN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7935BTPN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinC"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6377KNCH/",
"accession": "IGVFDS6377KNCH",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 35-45% expression of PPIF) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours, modified with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"purpose": "stimulation",
"summary": "Treatment of 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours",
"treatment_type": "protein"
},
{
"@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
"purpose": "stimulation",
"summary": "Treatment of 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "17",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:35:13.422866+00:00",
"summary": "cas mediated mutagenesis (Variant FlowFISH) integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "f7f1f2fc-675d-4e2b-818c-b1716303967b"
}