{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8168NPPI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8168NPPI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input_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 [IGVFDS8168NPPI](/measurement-sets/IGVFDS8168NPPI/) has sequence file(s) [IGVFFI8762KOWO](/sequence-files/IGVFFI8762KOWO/), [IGVFFI7787FZYH](/sequence-files/IGVFFI7787FZYH/), [IGVFFI4225DMAM](/sequence-files/IGVFFI4225DMAM/), [IGVFFI2259OLRW](/sequence-files/IGVFFI2259OLRW/), [IGVFFI7164SBNX](/sequence-files/IGVFFI7164SBNX/), [IGVFFI9626MSRO](/sequence-files/IGVFFI9626MSRO/), [IGVFFI5203XVMK](/sequence-files/IGVFFI5203XVMK/), [IGVFFI2212VWEB](/sequence-files/IGVFFI2212VWEB/) 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/IGVFDS8168NPPI/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8168NPPI](/measurement-sets/IGVFDS8168NPPI/) has sequence file(s): [IGVFFI8762KOWO](/sequence-files/IGVFFI8762KOWO/), [IGVFFI7787FZYH](/sequence-files/IGVFFI7787FZYH/), [IGVFFI4225DMAM](/sequence-files/IGVFFI4225DMAM/), [IGVFFI2259OLRW](/sequence-files/IGVFFI2259OLRW/), [IGVFFI7164SBNX](/sequence-files/IGVFFI7164SBNX/), [IGVFFI9626MSRO](/sequence-files/IGVFFI9626MSRO/), [IGVFFI5203XVMK](/sequence-files/IGVFFI5203XVMK/), [IGVFFI2212VWEB](/sequence-files/IGVFFI2212VWEB/) 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/IGVFDS8168NPPI/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1972TKGI](/in-vitro-systems/IGVFSM1972TKGI/) 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/IGVFSM1972TKGI/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8168NPPI](/measurement-sets/IGVFDS8168NPPI/) 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/IGVFDS8168NPPI/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS8168NPPI](/measurement-sets/IGVFDS8168NPPI/) 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/IGVFDS8168NPPI/"
}
]
},
"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": [],
"control_type": "unsorted FACS input",
"creation_timestamp": "2023-11-30T22:48:10.717421+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/IGVFFI8762KOWO/",
"accession": "IGVFFI8762KOWO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:24:51.515455+00:00",
"file_format": "fastq",
"file_size": 3430245,
"href": "/sequence-files/IGVFFI8762KOWO/@@download/IGVFFI8762KOWO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6c1b3292-cdbb-466c-b707-6866428efc4a/IGVFFI8762KOWO.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_S16-BioRep2-FFRep2-BinAll-PCRrep2_S197_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7787FZYH/",
"accession": "IGVFFI7787FZYH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:51:38.440736+00:00",
"file_format": "fastq",
"file_size": 3190608,
"href": "/sequence-files/IGVFFI7787FZYH/@@download/IGVFFI7787FZYH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a94ee0e1-4caf-484c-a202-ee872d5ff2f1/IGVFFI7787FZYH.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_S16-BioRep2-FFRep2-BinAll-PCRrep1_S140_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4225DMAM/",
"accession": "IGVFFI4225DMAM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:16:23.371398+00:00",
"file_format": "fastq",
"file_size": 14682912,
"href": "/sequence-files/IGVFFI4225DMAM/@@download/IGVFFI4225DMAM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5bc81d64-632d-4d79-a2b4-c55dbf7c0978/IGVFFI4225DMAM.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_S16-BioRep2-FFRep2-BinAll-PCRrep2_S197_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2259OLRW/",
"accession": "IGVFFI2259OLRW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:34:47.101944+00:00",
"file_format": "fastq",
"file_size": 7599443,
"href": "/sequence-files/IGVFFI2259OLRW/@@download/IGVFFI2259OLRW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/09965f82-239d-428b-8992-549dc2934f07/IGVFFI2259OLRW.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_S16-BioRep2-FFRep2-BinAll-PCRrep1_S140_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7164SBNX/",
"accession": "IGVFFI7164SBNX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:07:58.467980+00:00",
"file_format": "fastq",
"file_size": 7966869,
"href": "/sequence-files/IGVFFI7164SBNX/@@download/IGVFFI7164SBNX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/790d7c48-62ae-40a3-91a2-0853b73b4720/IGVFFI7164SBNX.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_S16-BioRep2-FFRep2-BinAll-PCRrep2_S197_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9626MSRO/",
"accession": "IGVFFI9626MSRO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:33:03.840219+00:00",
"file_format": "fastq",
"file_size": 3326401,
"href": "/sequence-files/IGVFFI9626MSRO/@@download/IGVFFI9626MSRO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/68fa0d4f-12a4-430f-9f84-0eaeaec7f734/IGVFFI9626MSRO.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_S16-BioRep2-FFRep2-BinAll-PCRrep2_S197_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5203XVMK/",
"accession": "IGVFFI5203XVMK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:43:11.607706+00:00",
"file_format": "fastq",
"file_size": 14072714,
"href": "/sequence-files/IGVFFI5203XVMK/@@download/IGVFFI5203XVMK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b4e51277-6114-4902-8b95-7ca3fe0b70c0/IGVFFI5203XVMK.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_S16-BioRep2-FFRep2-BinAll-PCRrep1_S140_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2212VWEB/",
"accession": "IGVFFI2212VWEB",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:59:45.474365+00:00",
"file_format": "fastq",
"file_size": 3168637,
"href": "/sequence-files/IGVFFI2212VWEB/@@download/IGVFFI2212VWEB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6096e8db-fd8f-4263-9af9-4a092bee421b/IGVFFI2212VWEB.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_S16-BioRep2-FFRep2-BinAll-PCRrep1_S140_I2_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": "2023-12-20T23:09:51.947212+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1972TKGI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1972TKGI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input"
],
"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 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), transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"status": "released",
"treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain"
},
{
"@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
"status": "released",
"treatment_term_name": "phorbol 13-acetate 12-myristate"
}
]
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:34:47.101944+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "158b5831-1b05-482a-9b72-fa96b988723a"
}