{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6538ISBQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6538ISBQ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-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 [IGVFDS6538ISBQ](/measurement-sets/IGVFDS6538ISBQ/) 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/IGVFDS6538ISBQ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6538ISBQ](/measurement-sets/IGVFDS6538ISBQ/) has sequence file(s) [IGVFFI4585NCVU](/sequence-files/IGVFFI4585NCVU/), [IGVFFI8945PBJY](/sequence-files/IGVFFI8945PBJY/), [IGVFFI5233ENIZ](/sequence-files/IGVFFI5233ENIZ/), [IGVFFI0092MDDO](/sequence-files/IGVFFI0092MDDO/), [IGVFFI2939WTHG](/sequence-files/IGVFFI2939WTHG/), [IGVFFI0763CVDI](/sequence-files/IGVFFI0763CVDI/), [IGVFFI3336NZFS](/sequence-files/IGVFFI3336NZFS/), [IGVFFI9541TIIT](/sequence-files/IGVFFI9541TIIT/) 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/IGVFDS6538ISBQ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6538ISBQ](/measurement-sets/IGVFDS6538ISBQ/) has sequence file(s): [IGVFFI4585NCVU](/sequence-files/IGVFFI4585NCVU/), [IGVFFI8945PBJY](/sequence-files/IGVFFI8945PBJY/), [IGVFFI5233ENIZ](/sequence-files/IGVFFI5233ENIZ/), [IGVFFI0092MDDO](/sequence-files/IGVFFI0092MDDO/), [IGVFFI2939WTHG](/sequence-files/IGVFFI2939WTHG/), [IGVFFI0763CVDI](/sequence-files/IGVFFI0763CVDI/), [IGVFFI3336NZFS](/sequence-files/IGVFFI3336NZFS/), [IGVFFI9541TIIT](/sequence-files/IGVFFI9541TIIT/) 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/IGVFDS6538ISBQ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM7602FHUT](/in-vitro-systems/IGVFSM7602FHUT/) 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/IGVFSM7602FHUT/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7602FHUT](/in-vitro-systems/IGVFSM7602FHUT/) 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/IGVFSM7602FHUT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing control for",
"detail": "Measurement set [IGVFDS6538ISBQ](/measurement-sets/IGVFDS6538ISBQ/) 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/IGVFDS6538ISBQ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6538ISBQ](/measurement-sets/IGVFDS6538ISBQ/) 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/IGVFDS6538ISBQ/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS6538ISBQ](/measurement-sets/IGVFDS6538ISBQ/) 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/IGVFDS6538ISBQ/"
}
]
},
"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": "2023-11-30T22:46:42.709093+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"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/IGVFFI4585NCVU/",
"accession": "IGVFFI4585NCVU",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:04:37.151584+00:00",
"file_format": "fastq",
"file_size": 3149236,
"href": "/sequence-files/IGVFFI4585NCVU/@@download/IGVFFI4585NCVU.fastq.gz",
"md5sum": "ff845cbfc203b01bfb849e051b757ac5",
"s3_uri": "s3://igvf-files/2023/12/05/72fa7a20-0fb8-4132-b99e-c667cf058533/IGVFFI4585NCVU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep1-BinAll-PCRrep2_S124_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8945PBJY/",
"accession": "IGVFFI8945PBJY",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:39:06.758559+00:00",
"file_format": "fastq",
"file_size": 8899274,
"href": "/sequence-files/IGVFFI8945PBJY/@@download/IGVFFI8945PBJY.fastq.gz",
"md5sum": "c76a10731af64311179561fbd21f69a8",
"s3_uri": "s3://igvf-files/2023/12/05/f2fcf6f0-c46e-4a50-879f-067ad5bb59dc/IGVFFI8945PBJY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep1-BinAll-PCRrep2_S124_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5233ENIZ/",
"accession": "IGVFFI5233ENIZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:51:58.612654+00:00",
"file_format": "fastq",
"file_size": 17352575,
"href": "/sequence-files/IGVFFI5233ENIZ/@@download/IGVFFI5233ENIZ.fastq.gz",
"md5sum": "f05d6fd7c030b157a48b02994e7704f6",
"s3_uri": "s3://igvf-files/2023/12/05/1a4e8d67-3926-41a6-b4e3-731c3bea086f/IGVFFI5233ENIZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep1-BinAll-PCRrep2_S124_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0092MDDO/",
"accession": "IGVFFI0092MDDO",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:16:52.868017+00:00",
"file_format": "fastq",
"file_size": 2991246,
"href": "/sequence-files/IGVFFI0092MDDO/@@download/IGVFFI0092MDDO.fastq.gz",
"md5sum": "31512387981fc0c5653c8ae032108ad3",
"s3_uri": "s3://igvf-files/2023/12/05/5e9d056d-69f4-4895-8982-72cd0c668e78/IGVFFI0092MDDO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep1-BinAll-PCRrep2_S124_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2939WTHG/",
"accession": "IGVFFI2939WTHG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:32:50.760532+00:00",
"file_format": "fastq",
"file_size": 8728749,
"href": "/sequence-files/IGVFFI2939WTHG/@@download/IGVFFI2939WTHG.fastq.gz",
"md5sum": "0badfd3b21cd04c3e826227665398baa",
"s3_uri": "s3://igvf-files/2023/12/05/7aff7e0d-285b-47a5-a6d3-0cf25b7a36ff/IGVFFI2939WTHG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep1-BinAll-PCRrep1_S28_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0763CVDI/",
"accession": "IGVFFI0763CVDI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:45:30.436912+00:00",
"file_format": "fastq",
"file_size": 16721201,
"href": "/sequence-files/IGVFFI0763CVDI/@@download/IGVFFI0763CVDI.fastq.gz",
"md5sum": "2b6ebcd82ab151dade5bfb69e5f2845a",
"s3_uri": "s3://igvf-files/2023/12/05/34c084eb-507f-43b9-ac6d-25e7476fb7e9/IGVFFI0763CVDI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep1-BinAll-PCRrep1_S28_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3336NZFS/",
"accession": "IGVFFI3336NZFS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:58:16.753115+00:00",
"file_format": "fastq",
"file_size": 3054498,
"href": "/sequence-files/IGVFFI3336NZFS/@@download/IGVFFI3336NZFS.fastq.gz",
"md5sum": "41622dd2bd4f32f3d0fb53446aa7f826",
"s3_uri": "s3://igvf-files/2023/12/05/3f3d5620-f429-4c94-9833-be9fd5b4f727/IGVFFI3336NZFS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep1-BinAll-PCRrep1_S28_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9541TIIT/",
"accession": "IGVFFI9541TIIT",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:10:46.823463+00:00",
"file_format": "fastq",
"file_size": 2873626,
"href": "/sequence-files/IGVFFI9541TIIT/@@download/IGVFFI9541TIIT.fastq.gz",
"md5sum": "aad172271551d2a49b3f0de01e0b3cac",
"s3_uri": "s3://igvf-files/2023/12/05/92a0644c-f254-420e-951c-a5fd6ef8cce9/IGVFFI9541TIIT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220426pPPIF_REPEAT-THP1-Gen8b-pPPIF-Amp_pPPIF-BioRep2-FFRep1-BinAll-PCRrep1_S28_I2_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": "2023-12-20T23:09:21.701148+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7602FHUT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7602FHUT",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-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": "2023-12-05T18:32:50.760532+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "087b9ec0-8940-44e5-a4ab-28aeecc9839f"
}