{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6473LUNY/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6473LUNY",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-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 [IGVFDS6473LUNY](/measurement-sets/IGVFDS6473LUNY/) 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/IGVFDS6473LUNY/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6473LUNY](/measurement-sets/IGVFDS6473LUNY/) has sequence file(s) [IGVFFI6012BDDS](/sequence-files/IGVFFI6012BDDS/), [IGVFFI7618TLJM](/sequence-files/IGVFFI7618TLJM/), [IGVFFI1717SMRK](/sequence-files/IGVFFI1717SMRK/), [IGVFFI0811JSXE](/sequence-files/IGVFFI0811JSXE/), [IGVFFI3496QCFY](/sequence-files/IGVFFI3496QCFY/), [IGVFFI7197VBPK](/sequence-files/IGVFFI7197VBPK/), [IGVFFI6186LNDG](/sequence-files/IGVFFI6186LNDG/), [IGVFFI1793FALM](/sequence-files/IGVFFI1793FALM/) 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/IGVFDS6473LUNY/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6473LUNY](/measurement-sets/IGVFDS6473LUNY/) has sequence file(s): [IGVFFI6012BDDS](/sequence-files/IGVFFI6012BDDS/), [IGVFFI7618TLJM](/sequence-files/IGVFFI7618TLJM/), [IGVFFI1717SMRK](/sequence-files/IGVFFI1717SMRK/), [IGVFFI0811JSXE](/sequence-files/IGVFFI0811JSXE/), [IGVFFI3496QCFY](/sequence-files/IGVFFI3496QCFY/), [IGVFFI7197VBPK](/sequence-files/IGVFFI7197VBPK/), [IGVFFI6186LNDG](/sequence-files/IGVFFI6186LNDG/), [IGVFFI1793FALM](/sequence-files/IGVFFI1793FALM/) 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/IGVFDS6473LUNY/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9808CICG](/in-vitro-systems/IGVFSM9808CICG/) 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/IGVFSM9808CICG/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM9808CICG](/in-vitro-systems/IGVFSM9808CICG/) 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/IGVFSM9808CICG/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing control for",
"detail": "Measurement set [IGVFDS6473LUNY](/measurement-sets/IGVFDS6473LUNY/) 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/IGVFDS6473LUNY/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6473LUNY](/measurement-sets/IGVFDS6473LUNY/) 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/IGVFDS6473LUNY/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS6473LUNY](/measurement-sets/IGVFDS6473LUNY/) 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/IGVFDS6473LUNY/"
}
]
},
"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/IGVFDS6385JXFZ/",
"accession": "IGVFDS6385JXFZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-THP1-PE2_Exp3_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"control_type": "unsorted FACS input",
"creation_timestamp": "2023-12-01T00:01:42.766626+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": [
{
"@id": "/sequence-files/IGVFFI6012BDDS/",
"accession": "IGVFFI6012BDDS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:59:34.032986+00:00",
"file_format": "fastq",
"file_size": 14485415,
"href": "/sequence-files/IGVFFI6012BDDS/@@download/IGVFFI6012BDDS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c5304cf7-c1da-41fa-b8cf-d118cabe7bbf/IGVFFI6012BDDS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-1-BinAll_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7618TLJM/",
"accession": "IGVFFI7618TLJM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:42:28.610521+00:00",
"file_format": "fastq",
"file_size": 73598335,
"href": "/sequence-files/IGVFFI7618TLJM/@@download/IGVFFI7618TLJM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f88f29f4-736c-4535-84d3-c56af04912c0/IGVFFI7618TLJM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-2-BinAll_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1717SMRK/",
"accession": "IGVFFI1717SMRK",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:05:06.071895+00:00",
"file_format": "fastq",
"file_size": 13791436,
"href": "/sequence-files/IGVFFI1717SMRK/@@download/IGVFFI1717SMRK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6183141e-bb7a-411e-832e-c86e91a74cdd/IGVFFI1717SMRK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-2-BinAll_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0811JSXE/",
"accession": "IGVFFI0811JSXE",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:53:54.143058+00:00",
"file_format": "fastq",
"file_size": 14818647,
"href": "/sequence-files/IGVFFI0811JSXE/@@download/IGVFFI0811JSXE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/09bfe5d3-a422-4b11-acc3-f3dfe3478ea7/IGVFFI0811JSXE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-2-BinAll_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3496QCFY/",
"accession": "IGVFFI3496QCFY",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:36:29.722230+00:00",
"file_format": "fastq",
"file_size": 77221342,
"href": "/sequence-files/IGVFFI3496QCFY/@@download/IGVFFI3496QCFY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e0fa1580-b626-4ac8-aea9-e8e5256e72e1/IGVFFI3496QCFY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-1-BinAll_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7197VBPK/",
"accession": "IGVFFI7197VBPK",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:30:39.504000+00:00",
"file_format": "fastq",
"file_size": 40757992,
"href": "/sequence-files/IGVFFI7197VBPK/@@download/IGVFFI7197VBPK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/34732be5-a3bf-4829-aca5-6b9905f9501e/IGVFFI7197VBPK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-2-BinAll_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6186LNDG/",
"accession": "IGVFFI6186LNDG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:24:56.237602+00:00",
"file_format": "fastq",
"file_size": 43087583,
"href": "/sequence-files/IGVFFI6186LNDG/@@download/IGVFFI6186LNDG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1728bb10-8ded-4334-93fc-06f9b58da8b1/IGVFFI6186LNDG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-1-BinAll_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1793FALM/",
"accession": "IGVFFI1793FALM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:48:21.149169+00:00",
"file_format": "fastq",
"file_size": 15708975,
"href": "/sequence-files/IGVFFI1793FALM/@@download/IGVFFI1793FALM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f832e250-3a56-464a-bb53-cce57b76ea62/IGVFFI1793FALM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-1-BinAll_I1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5056OAGR/"
],
"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": "2023-12-20T23:09:20.450127+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9808CICG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9808CICG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-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_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "Homo sapiens (male) THP-1 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": "2023-12-05T18:24:56.237602+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "be1f2662-3db9-4256-961e-a066e0196636"
}