{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6731AKUS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6731AKUS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-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 [IGVFSM0226JSRH](/in-vitro-systems/IGVFSM0226JSRH/) 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/IGVFSM0226JSRH/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0226JSRH](/in-vitro-systems/IGVFSM0226JSRH/) 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/IGVFSM0226JSRH/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS6731AKUS](/measurement-sets/IGVFDS6731AKUS/) 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/IGVFDS6731AKUS/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6731AKUS](/measurement-sets/IGVFDS6731AKUS/) has sequence file(s) [IGVFFI5600ZYMP](/sequence-files/IGVFFI5600ZYMP/), [IGVFFI4879FSVM](/sequence-files/IGVFFI4879FSVM/), [IGVFFI9393LMCL](/sequence-files/IGVFFI9393LMCL/), [IGVFFI0495TZPK](/sequence-files/IGVFFI0495TZPK/), [IGVFFI1397WGHI](/sequence-files/IGVFFI1397WGHI/), [IGVFFI6042JSEG](/sequence-files/IGVFFI6042JSEG/), [IGVFFI0835ASTY](/sequence-files/IGVFFI0835ASTY/), [IGVFFI2867KJCF](/sequence-files/IGVFFI2867KJCF/) 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/IGVFDS6731AKUS/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6731AKUS](/measurement-sets/IGVFDS6731AKUS/) has sequence file(s): [IGVFFI5600ZYMP](/sequence-files/IGVFFI5600ZYMP/), [IGVFFI4879FSVM](/sequence-files/IGVFFI4879FSVM/), [IGVFFI9393LMCL](/sequence-files/IGVFFI9393LMCL/), [IGVFFI0495TZPK](/sequence-files/IGVFFI0495TZPK/), [IGVFFI1397WGHI](/sequence-files/IGVFFI1397WGHI/), [IGVFFI6042JSEG](/sequence-files/IGVFFI6042JSEG/), [IGVFFI0835ASTY](/sequence-files/IGVFFI0835ASTY/), [IGVFFI2867KJCF](/sequence-files/IGVFFI2867KJCF/) 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/IGVFDS6731AKUS/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing control for",
"detail": "Measurement set [IGVFDS6731AKUS](/measurement-sets/IGVFDS6731AKUS/) 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/IGVFDS6731AKUS/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6731AKUS](/measurement-sets/IGVFDS6731AKUS/) 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/IGVFDS6731AKUS/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS6731AKUS](/measurement-sets/IGVFDS6731AKUS/) 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/IGVFDS6731AKUS/"
}
]
},
"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": "2023-11-30T22:45:55.148182+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/IGVFFI5600ZYMP/",
"accession": "IGVFFI5600ZYMP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:37:36.323279+00:00",
"file_format": "fastq",
"file_size": 73943067,
"href": "/sequence-files/IGVFFI5600ZYMP/@@download/IGVFFI5600ZYMP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/856b647e-814a-4da4-a73c-b49c2d90b171/IGVFFI5600ZYMP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-3-D21-pPPIF-Amp-pPPIF-1-2-1-BinAll_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4879FSVM/",
"accession": "IGVFFI4879FSVM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:54:58.502858+00:00",
"file_format": "fastq",
"file_size": 14942883,
"href": "/sequence-files/IGVFFI4879FSVM/@@download/IGVFFI4879FSVM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/749ebccb-cd04-4e12-8512-16a6050b5e80/IGVFFI4879FSVM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-3-D21-pPPIF-Amp-pPPIF-1-2-2-BinAll_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9393LMCL/",
"accession": "IGVFFI9393LMCL",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:06:13.939587+00:00",
"file_format": "fastq",
"file_size": 14042930,
"href": "/sequence-files/IGVFFI9393LMCL/@@download/IGVFFI9393LMCL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/537c2773-a035-4cc9-a571-b7e2343cd38c/IGVFFI9393LMCL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-3-D21-pPPIF-Amp-pPPIF-1-2-2-BinAll_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0495TZPK/",
"accession": "IGVFFI0495TZPK",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:49:24.817037+00:00",
"file_format": "fastq",
"file_size": 14875932,
"href": "/sequence-files/IGVFFI0495TZPK/@@download/IGVFFI0495TZPK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2ecbba96-b11f-40e9-b906-70ed48ee339d/IGVFFI0495TZPK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-3-D21-pPPIF-Amp-pPPIF-1-2-1-BinAll_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1397WGHI/",
"accession": "IGVFFI1397WGHI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:31:45.464395+00:00",
"file_format": "fastq",
"file_size": 42224982,
"href": "/sequence-files/IGVFFI1397WGHI/@@download/IGVFFI1397WGHI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fbc05658-8616-4370-8970-6a4c1003342d/IGVFFI1397WGHI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-3-D21-pPPIF-Amp-pPPIF-1-2-2-BinAll_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6042JSEG/",
"accession": "IGVFFI6042JSEG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:00:39.457164+00:00",
"file_format": "fastq",
"file_size": 13832661,
"href": "/sequence-files/IGVFFI6042JSEG/@@download/IGVFFI6042JSEG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9754013c-0113-4d66-bad5-e524d913099b/IGVFFI6042JSEG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-3-D21-pPPIF-Amp-pPPIF-1-2-1-BinAll_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0835ASTY/",
"accession": "IGVFFI0835ASTY",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:43:40.792880+00:00",
"file_format": "fastq",
"file_size": 75463196,
"href": "/sequence-files/IGVFFI0835ASTY/@@download/IGVFFI0835ASTY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e8453590-14e2-4b4f-a35e-f5aaa06cc66c/IGVFFI0835ASTY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-3-D21-pPPIF-Amp-pPPIF-1-2-2-BinAll_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2867KJCF/",
"accession": "IGVFFI2867KJCF",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:26:01.315472+00:00",
"file_format": "fastq",
"file_size": 41266483,
"href": "/sequence-files/IGVFFI2867KJCF/@@download/IGVFFI2867KJCF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/65799a4a-6ddd-4caa-96ed-d4e7b654b9e2/IGVFFI2867KJCF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-3-D21-pPPIF-Amp-pPPIF-1-2-1-BinAll_R1_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": "2023-12-20T23:09:39.551248+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0226JSRH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0226JSRH",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-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_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": "2023-12-05T18:26:01.315472+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "a892e011-0683-4ae1-8543-c7a2fe3e5a26"
}