{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9345IHWB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9345IHWB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-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": "mismatched status",
"detail": "Released in vitro system [IGVFSM8585CWCE](/in-vitro-systems/IGVFSM8585CWCE/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM8585CWCE/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM8585CWCE](/in-vitro-systems/IGVFSM8585CWCE/) 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/IGVFSM8585CWCE/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9345IHWB](/measurement-sets/IGVFDS9345IHWB/) 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/IGVFDS9345IHWB/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9345IHWB](/measurement-sets/IGVFDS9345IHWB/) has sequence file(s) [IGVFFI6991YAWV](/sequence-files/IGVFFI6991YAWV/), [IGVFFI1508PMWB](/sequence-files/IGVFFI1508PMWB/), [IGVFFI7766HSCT](/sequence-files/IGVFFI7766HSCT/), [IGVFFI9805BFHG](/sequence-files/IGVFFI9805BFHG/), [IGVFFI9535DKUV](/sequence-files/IGVFFI9535DKUV/), [IGVFFI0074KQGV](/sequence-files/IGVFFI0074KQGV/), [IGVFFI8853XKZC](/sequence-files/IGVFFI8853XKZC/), [IGVFFI6676TULQ](/sequence-files/IGVFFI6676TULQ/) 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/IGVFDS9345IHWB/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9345IHWB](/measurement-sets/IGVFDS9345IHWB/) has sequence file(s): [IGVFFI6991YAWV](/sequence-files/IGVFFI6991YAWV/), [IGVFFI1508PMWB](/sequence-files/IGVFFI1508PMWB/), [IGVFFI7766HSCT](/sequence-files/IGVFFI7766HSCT/), [IGVFFI9805BFHG](/sequence-files/IGVFFI9805BFHG/), [IGVFFI9535DKUV](/sequence-files/IGVFFI9535DKUV/), [IGVFFI0074KQGV](/sequence-files/IGVFFI0074KQGV/), [IGVFFI8853XKZC](/sequence-files/IGVFFI8853XKZC/), [IGVFFI6676TULQ](/sequence-files/IGVFFI6676TULQ/) 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/IGVFDS9345IHWB/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing control for",
"detail": "Measurement set [IGVFDS9345IHWB](/measurement-sets/IGVFDS9345IHWB/) 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/IGVFDS9345IHWB/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9345IHWB](/measurement-sets/IGVFDS9345IHWB/) 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/IGVFDS9345IHWB/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS9345IHWB](/measurement-sets/IGVFDS9345IHWB/) 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/IGVFDS9345IHWB/"
}
]
},
"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/IGVFDS2374NXLW/",
"accession": "IGVFDS2374NXLW",
"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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"control_type": "unsorted FACS input",
"creation_timestamp": "2023-12-01T00:04:42.296355+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/IGVFFI6991YAWV/",
"accession": "IGVFFI6991YAWV",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:17:52.814511+00:00",
"file_format": "fastq",
"file_size": 3598294,
"href": "/sequence-files/IGVFFI6991YAWV/@@download/IGVFFI6991YAWV.fastq.gz",
"md5sum": "920a5588a7d2baaf233d19c1ffc7829f",
"s3_uri": "s3://igvf-files/2023/12/05/92a076e3-0a26-4824-bfad-be7e7b513324/IGVFFI6991YAWV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinAll-PCRrep2_S395_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1508PMWB/",
"accession": "IGVFFI1508PMWB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:17:15.741247+00:00",
"file_format": "fastq",
"file_size": 3390309,
"href": "/sequence-files/IGVFFI1508PMWB/@@download/IGVFFI1508PMWB.fastq.gz",
"md5sum": "0f8d050e21cc1019549f59288a4664ac",
"s3_uri": "s3://igvf-files/2023/12/05/c50bd4ca-db65-47e3-95ff-0465bb485df2/IGVFFI1508PMWB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinAll-PCRrep1_S385_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7766HSCT/",
"accession": "IGVFFI7766HSCT",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:17:34.419611+00:00",
"file_format": "fastq",
"file_size": 996256,
"href": "/sequence-files/IGVFFI7766HSCT/@@download/IGVFFI7766HSCT.fastq.gz",
"md5sum": "05338e76a885fd15ebc94aab769227e9",
"s3_uri": "s3://igvf-files/2023/12/05/3b8a9331-a761-4f1d-adc5-b3e6d770119b/IGVFFI7766HSCT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinAll-PCRrep2_S395_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9805BFHG/",
"accession": "IGVFFI9805BFHG",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:17:24.974300+00:00",
"file_format": "fastq",
"file_size": 4007059,
"href": "/sequence-files/IGVFFI9805BFHG/@@download/IGVFFI9805BFHG.fastq.gz",
"md5sum": "dbde59b65da08c1c5aa166dca02321ad",
"s3_uri": "s3://igvf-files/2023/12/05/6bf1fc4e-5466-43b6-a8ef-b2cc964c1ff3/IGVFFI9805BFHG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinAll-PCRrep1_S385_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9535DKUV/",
"accession": "IGVFFI9535DKUV",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:17:06.719416+00:00",
"file_format": "fastq",
"file_size": 899659,
"href": "/sequence-files/IGVFFI9535DKUV/@@download/IGVFFI9535DKUV.fastq.gz",
"md5sum": "21cc95fd72ed803a494582ec9cd45cb4",
"s3_uri": "s3://igvf-files/2023/12/05/4fcc8842-4fbe-4de4-b282-16aad26a21cc/IGVFFI9535DKUV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinAll-PCRrep1_S385_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0074KQGV/",
"accession": "IGVFFI0074KQGV",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:17:43.549358+00:00",
"file_format": "fastq",
"file_size": 951682,
"href": "/sequence-files/IGVFFI0074KQGV/@@download/IGVFFI0074KQGV.fastq.gz",
"md5sum": "668b72849bfd23e4ec0d81f7d63163e0",
"s3_uri": "s3://igvf-files/2023/12/05/dd472d8e-e86f-4c80-80e0-17ad4bac037d/IGVFFI0074KQGV.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinAll-PCRrep2_S395_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8853XKZC/",
"accession": "IGVFFI8853XKZC",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:18:02.259751+00:00",
"file_format": "fastq",
"file_size": 4274317,
"href": "/sequence-files/IGVFFI8853XKZC/@@download/IGVFFI8853XKZC.fastq.gz",
"md5sum": "44ba23a8871ae4647d2e9c3ac5c3cee5",
"s3_uri": "s3://igvf-files/2023/12/05/cc0d25ff-bd2f-4329-b27d-73575db609f1/IGVFFI8853XKZC.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinAll-PCRrep2_S395_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6676TULQ/",
"accession": "IGVFFI6676TULQ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:16:57.726679+00:00",
"file_format": "fastq",
"file_size": 880394,
"href": "/sequence-files/IGVFFI6676TULQ/@@download/IGVFFI6676TULQ.fastq.gz",
"md5sum": "3d071bad0506846644e39e111a1099a8",
"s3_uri": "s3://igvf-files/2023/12/05/2f6c1e51-feab-466a-a1cd-820b2ce3ad9a/IGVFFI6676TULQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinAll-PCRrep1_S385_I1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5031MNRR/"
],
"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": "2023-12-20T23:05:34.567847+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8585CWCE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8585CWCE",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-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": "2023-12-05T19:16:57.726679+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "46f2d31f-ee6c-4bdb-852c-846f09802f4c"
}