{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8499AVHV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8499AVHV",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-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": "mismatched status",
"detail": "Released in vitro system [IGVFSM6600KXOT](/in-vitro-systems/IGVFSM6600KXOT/) 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/IGVFSM6600KXOT/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8499AVHV](/measurement-sets/IGVFDS8499AVHV/) has sequence file(s) [IGVFFI7621VYXX](/sequence-files/IGVFFI7621VYXX/), [IGVFFI3658DGDG](/sequence-files/IGVFFI3658DGDG/), [IGVFFI0260SGJC](/sequence-files/IGVFFI0260SGJC/), [IGVFFI0554KWNV](/sequence-files/IGVFFI0554KWNV/), [IGVFFI3438UDKD](/sequence-files/IGVFFI3438UDKD/), [IGVFFI3530KETI](/sequence-files/IGVFFI3530KETI/), [IGVFFI8337IPNV](/sequence-files/IGVFFI8337IPNV/), [IGVFFI3475HRSR](/sequence-files/IGVFFI3475HRSR/) 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/IGVFDS8499AVHV/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8499AVHV](/measurement-sets/IGVFDS8499AVHV/) has sequence file(s): [IGVFFI7621VYXX](/sequence-files/IGVFFI7621VYXX/), [IGVFFI3658DGDG](/sequence-files/IGVFFI3658DGDG/), [IGVFFI0260SGJC](/sequence-files/IGVFFI0260SGJC/), [IGVFFI0554KWNV](/sequence-files/IGVFFI0554KWNV/), [IGVFFI3438UDKD](/sequence-files/IGVFFI3438UDKD/), [IGVFFI3530KETI](/sequence-files/IGVFFI3530KETI/), [IGVFFI8337IPNV](/sequence-files/IGVFFI8337IPNV/), [IGVFFI3475HRSR](/sequence-files/IGVFFI3475HRSR/) 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/IGVFDS8499AVHV/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8499AVHV](/measurement-sets/IGVFDS8499AVHV/) 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/IGVFDS8499AVHV/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS8499AVHV](/measurement-sets/IGVFDS8499AVHV/) 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/IGVFDS8499AVHV/"
}
]
},
"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/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"control_type": "unsorted FACS input",
"creation_timestamp": "2023-12-13T08:01:44.599139+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
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"accession": "IGVFFI7621VYXX",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T16:37:14.069633+00:00",
"file_format": "fastq",
"file_size": 1997961,
"href": "/sequence-files/IGVFFI7621VYXX/@@download/IGVFFI7621VYXX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/0521d0c2-26ec-494d-9db1-bfa5d2b8e54b/IGVFFI7621VYXX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep1_BinAll-PCRrep2_S394_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3658DGDG/",
"accession": "IGVFFI3658DGDG",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T08:51:49.351362+00:00",
"file_format": "fastq",
"file_size": 8870460,
"href": "/sequence-files/IGVFFI3658DGDG/@@download/IGVFFI3658DGDG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/bf696517-3530-4508-a3cd-85a15136b044/IGVFFI3658DGDG.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep1_BinAll-PCRrep2_S394_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0260SGJC/",
"accession": "IGVFFI0260SGJC",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T09:59:03.604250+00:00",
"file_format": "fastq",
"file_size": 12022379,
"href": "/sequence-files/IGVFFI0260SGJC/@@download/IGVFFI0260SGJC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/86f52ac4-888c-4f9d-8a3b-874006624e0f/IGVFFI0260SGJC.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep1_BinAll-PCRrep1_S393_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0554KWNV/",
"accession": "IGVFFI0554KWNV",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T08:50:59.502105+00:00",
"file_format": "fastq",
"file_size": 9559232,
"href": "/sequence-files/IGVFFI0554KWNV/@@download/IGVFFI0554KWNV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/91871326-de4d-4e3e-a38b-362aa32c9adc/IGVFFI0554KWNV.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep1_BinAll-PCRrep1_S393_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3438UDKD/",
"accession": "IGVFFI3438UDKD",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T15:33:35.309355+00:00",
"file_format": "fastq",
"file_size": 2018340,
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"s3_uri": "s3://igvf-files/2023/12/13/f8ad96ba-c4cf-4720-84c9-2c7fa063c300/IGVFFI3438UDKD.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep1_BinAll-PCRrep2_S394_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3530KETI/",
"accession": "IGVFFI3530KETI",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T15:32:47.839428+00:00",
"file_format": "fastq",
"file_size": 2252241,
"href": "/sequence-files/IGVFFI3530KETI/@@download/IGVFFI3530KETI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/13/1696a4b1-89eb-4e70-8fb0-513d44a10f00/IGVFFI3530KETI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep1_BinAll-PCRrep1_S393_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8337IPNV/",
"accession": "IGVFFI8337IPNV",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T09:59:57.218822+00:00",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep1_BinAll-PCRrep2_S394_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3475HRSR/",
"accession": "IGVFFI3475HRSR",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T16:36:26.838086+00:00",
"file_format": "fastq",
"file_size": 2142033,
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep2-FFRep1_BinAll-PCRrep1_S393_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4359OODY/"
],
"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": "2023-12-20T23:07:34.231445+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6600KXOT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6600KXOT",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-FACS_Input"
],
"classifications": [
"cell line"
],
"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"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "THP-1 cell line, male, Homo sapiens 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": "2023-12-13T08:50:59.502105+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "6d0e8cd7-046e-46e9-beca-aaff7c25dd6f"
}