{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5504TLBF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5504TLBF",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-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": "mismatched status",
"detail": "Released in vitro system [IGVFSM4816WKOM](/in-vitro-systems/IGVFSM4816WKOM/) has in progress subobject construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM4816WKOM/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM4816WKOM](/in-vitro-systems/IGVFSM4816WKOM/) 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/IGVFSM4816WKOM/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS5504TLBF](/measurement-sets/IGVFDS5504TLBF/) 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/IGVFDS5504TLBF/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5504TLBF](/measurement-sets/IGVFDS5504TLBF/) has sequence file(s) [IGVFFI5766MGLF](/sequence-files/IGVFFI5766MGLF/), [IGVFFI8547DRGU](/sequence-files/IGVFFI8547DRGU/), [IGVFFI6304IQEY](/sequence-files/IGVFFI6304IQEY/), [IGVFFI3078MPUG](/sequence-files/IGVFFI3078MPUG/), [IGVFFI4330ZBXH](/sequence-files/IGVFFI4330ZBXH/), [IGVFFI0292WJMY](/sequence-files/IGVFFI0292WJMY/), [IGVFFI9520FTLK](/sequence-files/IGVFFI9520FTLK/), [IGVFFI1898QNUG](/sequence-files/IGVFFI1898QNUG/) 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/IGVFDS5504TLBF/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5504TLBF](/measurement-sets/IGVFDS5504TLBF/) has sequence file(s): [IGVFFI5766MGLF](/sequence-files/IGVFFI5766MGLF/), [IGVFFI8547DRGU](/sequence-files/IGVFFI8547DRGU/), [IGVFFI6304IQEY](/sequence-files/IGVFFI6304IQEY/), [IGVFFI3078MPUG](/sequence-files/IGVFFI3078MPUG/), [IGVFFI4330ZBXH](/sequence-files/IGVFFI4330ZBXH/), [IGVFFI0292WJMY](/sequence-files/IGVFFI0292WJMY/), [IGVFFI9520FTLK](/sequence-files/IGVFFI9520FTLK/), [IGVFFI1898QNUG](/sequence-files/IGVFFI1898QNUG/) 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/IGVFDS5504TLBF/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing control for",
"detail": "Measurement set [IGVFDS5504TLBF](/measurement-sets/IGVFDS5504TLBF/) 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/IGVFDS5504TLBF/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5504TLBF](/measurement-sets/IGVFDS5504TLBF/) 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/IGVFDS5504TLBF/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS5504TLBF](/measurement-sets/IGVFDS5504TLBF/) 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/IGVFDS5504TLBF/"
}
]
},
"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/IGVFDS2385DHZO/",
"accession": "IGVFDS2385DHZO",
"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/IGVFDS4869FXYY/",
"accession": "IGVFDS4869FXYY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"control_type": "unsorted FACS input",
"creation_timestamp": "2023-12-13T08:48:05.926497+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/IGVFFI5766MGLF/",
"accession": "IGVFFI5766MGLF",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T15:11:56.252442+00:00",
"file_format": "fastq",
"file_size": 2026324,
"href": "/sequence-files/IGVFFI5766MGLF/@@download/IGVFFI5766MGLF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/fb85f2aa-c2f3-4021-8359-ca86361983d0/IGVFFI5766MGLF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep2_BinAll-PCRrep2_S388_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8547DRGU/",
"accession": "IGVFFI8547DRGU",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T10:42:03.979594+00:00",
"file_format": "fastq",
"file_size": 9145751,
"href": "/sequence-files/IGVFFI8547DRGU/@@download/IGVFFI8547DRGU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/54548a0d-ee9c-466d-a949-020384ed7b9b/IGVFFI8547DRGU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep2_BinAll-PCRrep1_S387_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6304IQEY/",
"accession": "IGVFFI6304IQEY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T16:14:43.184741+00:00",
"file_format": "fastq",
"file_size": 1958966,
"href": "/sequence-files/IGVFFI6304IQEY/@@download/IGVFFI6304IQEY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/5aaf3340-ac55-4ce7-becd-4a41969ba05c/IGVFFI6304IQEY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep2_BinAll-PCRrep2_S388_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3078MPUG/",
"accession": "IGVFFI3078MPUG",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T16:13:56.804244+00:00",
"file_format": "fastq",
"file_size": 1830494,
"href": "/sequence-files/IGVFFI3078MPUG/@@download/IGVFFI3078MPUG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/a677ccf0-3ed2-47fd-85d7-c159c372a719/IGVFFI3078MPUG.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep2_BinAll-PCRrep1_S387_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4330ZBXH/",
"accession": "IGVFFI4330ZBXH",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T09:37:54.262191+00:00",
"file_format": "fastq",
"file_size": 6982306,
"href": "/sequence-files/IGVFFI4330ZBXH/@@download/IGVFFI4330ZBXH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/9eff69ec-d531-4c5e-95b0-3f4c7e3aafdb/IGVFFI4330ZBXH.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep2_BinAll-PCRrep2_S388_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0292WJMY/",
"accession": "IGVFFI0292WJMY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T09:37:06.463960+00:00",
"file_format": "fastq",
"file_size": 6622293,
"href": "/sequence-files/IGVFFI0292WJMY/@@download/IGVFFI0292WJMY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/b652ed17-ac44-4ca1-a28d-4d6646e5c9c8/IGVFFI0292WJMY.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep2_BinAll-PCRrep1_S387_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9520FTLK/",
"accession": "IGVFFI9520FTLK",
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T15:11:09.160429+00:00",
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"s3_uri": "s3://igvf-files/2023/12/13/7ff407fa-48eb-4b89-877d-c89e86248542/IGVFFI9520FTLK.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
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"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep2_BinAll-PCRrep1_S387_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1898QNUG/",
"accession": "IGVFFI1898QNUG",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T10:42:52.913796+00:00",
"file_format": "fastq",
"file_size": 9549023,
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep2_BinAll-PCRrep2_S388_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6299IJHG/"
],
"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": "2023-12-20T23:08:12.937031+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4816WKOM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4816WKOM",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-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 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": "2023-12-13T09:37:06.463960+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "bfe34d6a-01b5-44fe-ad7a-3ac97fffe9af"
}