{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9063BNOD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9063BNOD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-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 [IGVFDS9063BNOD](/measurement-sets/IGVFDS9063BNOD/) 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/IGVFDS9063BNOD/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9063BNOD](/measurement-sets/IGVFDS9063BNOD/) has sequence file(s) [IGVFFI6251YWFF](/sequence-files/IGVFFI6251YWFF/), [IGVFFI3714JMPE](/sequence-files/IGVFFI3714JMPE/), [IGVFFI5559VJME](/sequence-files/IGVFFI5559VJME/), [IGVFFI8049YCGY](/sequence-files/IGVFFI8049YCGY/), [IGVFFI2704VWGC](/sequence-files/IGVFFI2704VWGC/), [IGVFFI5458GZAF](/sequence-files/IGVFFI5458GZAF/), [IGVFFI4550DTOI](/sequence-files/IGVFFI4550DTOI/), [IGVFFI5939NXVC](/sequence-files/IGVFFI5939NXVC/) 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/IGVFDS9063BNOD/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9063BNOD](/measurement-sets/IGVFDS9063BNOD/) has sequence file(s): [IGVFFI6251YWFF](/sequence-files/IGVFFI6251YWFF/), [IGVFFI3714JMPE](/sequence-files/IGVFFI3714JMPE/), [IGVFFI5559VJME](/sequence-files/IGVFFI5559VJME/), [IGVFFI8049YCGY](/sequence-files/IGVFFI8049YCGY/), [IGVFFI2704VWGC](/sequence-files/IGVFFI2704VWGC/), [IGVFFI5458GZAF](/sequence-files/IGVFFI5458GZAF/), [IGVFFI4550DTOI](/sequence-files/IGVFFI4550DTOI/), [IGVFFI5939NXVC](/sequence-files/IGVFFI5939NXVC/) 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/IGVFDS9063BNOD/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8422VLKL](/in-vitro-systems/IGVFSM8422VLKL/) 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/IGVFSM8422VLKL/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM8422VLKL](/in-vitro-systems/IGVFSM8422VLKL/) 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/IGVFSM8422VLKL/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing control for",
"detail": "Measurement set [IGVFDS9063BNOD](/measurement-sets/IGVFDS9063BNOD/) 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/IGVFDS9063BNOD/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9063BNOD](/measurement-sets/IGVFDS9063BNOD/) 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/IGVFDS9063BNOD/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS9063BNOD](/measurement-sets/IGVFDS9063BNOD/) 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/IGVFDS9063BNOD/"
}
]
},
"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/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"
],
"status": "released"
}
],
"control_for": [],
"control_type": "unsorted FACS input",
"creation_timestamp": "2023-11-30T22:48:25.991780+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI6251YWFF/",
"accession": "IGVFFI6251YWFF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:18:30.961922+00:00",
"file_format": "fastq",
"file_size": 14320963,
"href": "/sequence-files/IGVFFI6251YWFF/@@download/IGVFFI6251YWFF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3e34b95e-3960-45b3-9693-b5073b88f558/IGVFFI6251YWFF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinAll-PCRrep2_S211_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3714JMPE/",
"accession": "IGVFFI3714JMPE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:35:06.618445+00:00",
"file_format": "fastq",
"file_size": 3164062,
"href": "/sequence-files/IGVFFI3714JMPE/@@download/IGVFFI3714JMPE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e4399507-6151-4f59-b541-89a6d5d336fb/IGVFFI3714JMPE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinAll-PCRrep2_S211_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5559VJME/",
"accession": "IGVFFI5559VJME",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:53:40.086515+00:00",
"file_format": "fastq",
"file_size": 3305020,
"href": "/sequence-files/IGVFFI5559VJME/@@download/IGVFFI5559VJME.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4dc225e2-d7ee-443d-8ba4-36b61962efa5/IGVFFI5559VJME.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinAll-PCRrep1_S154_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8049YCGY/",
"accession": "IGVFFI8049YCGY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:36:51.060002+00:00",
"file_format": "fastq",
"file_size": 7699426,
"href": "/sequence-files/IGVFFI8049YCGY/@@download/IGVFFI8049YCGY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5a28631a-b6f1-4ec9-876b-305140296383/IGVFFI8049YCGY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinAll-PCRrep1_S154_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2704VWGC/",
"accession": "IGVFFI2704VWGC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:26:53.503163+00:00",
"file_format": "fastq",
"file_size": 3322285,
"href": "/sequence-files/IGVFFI2704VWGC/@@download/IGVFFI2704VWGC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b7a22dd6-c898-4f8e-9abc-a1833e3f3942/IGVFFI2704VWGC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinAll-PCRrep2_S211_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5458GZAF/",
"accession": "IGVFFI5458GZAF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:10:02.288313+00:00",
"file_format": "fastq",
"file_size": 7553964,
"href": "/sequence-files/IGVFFI5458GZAF/@@download/IGVFFI5458GZAF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/78f52f7d-caf0-482a-8c0c-9f6bf2e8f4ef/IGVFFI5458GZAF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinAll-PCRrep2_S211_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4550DTOI/",
"accession": "IGVFFI4550DTOI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:01:47.655926+00:00",
"file_format": "fastq",
"file_size": 3211762,
"href": "/sequence-files/IGVFFI4550DTOI/@@download/IGVFFI4550DTOI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e7016530-bec1-4560-a3d4-f8f384b6c10f/IGVFFI4550DTOI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinAll-PCRrep1_S154_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5939NXVC/",
"accession": "IGVFFI5939NXVC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:45:19.929136+00:00",
"file_format": "fastq",
"file_size": 14212919,
"href": "/sequence-files/IGVFFI5939NXVC/@@download/IGVFFI5939NXVC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ce0e6a39-949d-428b-96f6-ea6996cdb419/IGVFFI5939NXVC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinAll-PCRrep1_S154_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_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. 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": "2023-12-20T23:11:11.121274+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8422VLKL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8422VLKL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-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_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Homo sapiens (male) Jurkat cell line 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 CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"purpose": "stimulation",
"status": "released",
"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",
"status": "released",
"summary": "Treatment of 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:36:51.060002+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "af7e3ddf-cfcf-4ba7-a66d-5124c0d24314"
}