{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0120YHME/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0120YHME",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA_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 [IGVFDS0120YHME](/measurement-sets/IGVFDS0120YHME/) has sequence file(s) [IGVFFI8471SQCM](/sequence-files/IGVFFI8471SQCM/), [IGVFFI0523CAKB](/sequence-files/IGVFFI0523CAKB/), [IGVFFI2987HUNV](/sequence-files/IGVFFI2987HUNV/), [IGVFFI0174SRME](/sequence-files/IGVFFI0174SRME/), [IGVFFI8572LIGU](/sequence-files/IGVFFI8572LIGU/), [IGVFFI1659GJXT](/sequence-files/IGVFFI1659GJXT/), [IGVFFI1487ILZL](/sequence-files/IGVFFI1487ILZL/), [IGVFFI0536RYTX](/sequence-files/IGVFFI0536RYTX/) 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/IGVFDS0120YHME/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0120YHME](/measurement-sets/IGVFDS0120YHME/) has sequence file(s): [IGVFFI8471SQCM](/sequence-files/IGVFFI8471SQCM/), [IGVFFI0523CAKB](/sequence-files/IGVFFI0523CAKB/), [IGVFFI2987HUNV](/sequence-files/IGVFFI2987HUNV/), [IGVFFI0174SRME](/sequence-files/IGVFFI0174SRME/), [IGVFFI8572LIGU](/sequence-files/IGVFFI8572LIGU/), [IGVFFI1659GJXT](/sequence-files/IGVFFI1659GJXT/), [IGVFFI1487ILZL](/sequence-files/IGVFFI1487ILZL/), [IGVFFI0536RYTX](/sequence-files/IGVFFI0536RYTX/) 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/IGVFDS0120YHME/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM4133KDLM](/in-vitro-systems/IGVFSM4133KDLM/) 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/IGVFSM4133KDLM/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0120YHME](/measurement-sets/IGVFDS0120YHME/) 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/IGVFDS0120YHME/"
}
]
},
"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"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:47:14.893103+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/IGVFFI8471SQCM/",
"accession": "IGVFFI8471SQCM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:41:56.611093+00:00",
"file_format": "fastq",
"file_size": 7699605,
"href": "/sequence-files/IGVFFI8471SQCM/@@download/IGVFFI8471SQCM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1cd70039-f69e-468e-8552-d510efd3a042/IGVFFI8471SQCM.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_pPPIF_S5-BioRep2-FFRep1-BinA-PCRrep1_S15_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0523CAKB/",
"accession": "IGVFFI0523CAKB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:13:55.779178+00:00",
"file_format": "fastq",
"file_size": 3334248,
"href": "/sequence-files/IGVFFI0523CAKB/@@download/IGVFFI0523CAKB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/483169f2-ce0e-4712-ae4b-ffca0e69ef23/IGVFFI0523CAKB.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_pPPIF_S5-BioRep2-FFRep1-BinA-PCRrep2_S71_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2987HUNV/",
"accession": "IGVFFI2987HUNV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:48:14.994003+00:00",
"file_format": "fastq",
"file_size": 7856990,
"href": "/sequence-files/IGVFFI2987HUNV/@@download/IGVFFI2987HUNV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a2e9fd82-d84a-4a71-8ef7-ee904d0dc0ca/IGVFFI2987HUNV.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_pPPIF_S5-BioRep2-FFRep1-BinA-PCRrep2_S71_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0174SRME/",
"accession": "IGVFFI0174SRME",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:20:11.230864+00:00",
"file_format": "fastq",
"file_size": 3116176,
"href": "/sequence-files/IGVFFI0174SRME/@@download/IGVFFI0174SRME.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9539f913-88b7-44c9-ba8a-9fd4242c5938/IGVFFI0174SRME.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_pPPIF_S5-BioRep2-FFRep1-BinA-PCRrep1_S15_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8572LIGU/",
"accession": "IGVFFI8572LIGU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:01:15.566185+00:00",
"file_format": "fastq",
"file_size": 14281631,
"href": "/sequence-files/IGVFFI8572LIGU/@@download/IGVFFI8572LIGU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a8063324-a50d-4eba-85a6-902d6c0e101f/IGVFFI8572LIGU.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_pPPIF_S5-BioRep2-FFRep1-BinA-PCRrep2_S71_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1659GJXT/",
"accession": "IGVFFI1659GJXT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:54:38.094124+00:00",
"file_format": "fastq",
"file_size": 13949069,
"href": "/sequence-files/IGVFFI1659GJXT/@@download/IGVFFI1659GJXT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/13dac7fd-772c-4573-8b70-cd6349c2b08d/IGVFFI1659GJXT.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_pPPIF_S5-BioRep2-FFRep1-BinA-PCRrep1_S15_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1487ILZL/",
"accession": "IGVFFI1487ILZL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:07:40.963677+00:00",
"file_format": "fastq",
"file_size": 3142539,
"href": "/sequence-files/IGVFFI1487ILZL/@@download/IGVFFI1487ILZL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1f196ef8-0721-46b3-b4bb-5e5168944749/IGVFFI1487ILZL.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_pPPIF_S5-BioRep2-FFRep1-BinA-PCRrep1_S15_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0536RYTX/",
"accession": "IGVFFI0536RYTX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:26:31.898855+00:00",
"file_format": "fastq",
"file_size": 3166111,
"href": "/sequence-files/IGVFFI0536RYTX/@@download/IGVFFI0536RYTX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5e30bf92-c926-4f98-88f1-ec7b7e82a95b/IGVFFI0536RYTX.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_pPPIF_S5-BioRep2-FFRep1-BinA-PCRrep2_S71_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9162RHFP/"
],
"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": "2023-12-20T23:03:39.125133+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4133KDLM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4133KDLM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinA"
],
"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_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 0-10% 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": "2023-12-05T18:41:56.611093+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": "cca32d78-ea12-41cd-9ba1-0e3886feca00"
}