{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1696YMUM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1696YMUM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-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 [IGVFSM1355ITKK](/in-vitro-systems/IGVFSM1355ITKK/) 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/IGVFSM1355ITKK/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1355ITKK](/in-vitro-systems/IGVFSM1355ITKK/) 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/IGVFSM1355ITKK/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS1696YMUM](/measurement-sets/IGVFDS1696YMUM/) 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/IGVFDS1696YMUM/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1696YMUM](/measurement-sets/IGVFDS1696YMUM/) has sequence file(s) [IGVFFI2690GYIJ](/sequence-files/IGVFFI2690GYIJ/), [IGVFFI8494NBYO](/sequence-files/IGVFFI8494NBYO/), [IGVFFI1443GCTE](/sequence-files/IGVFFI1443GCTE/), [IGVFFI3604KHTE](/sequence-files/IGVFFI3604KHTE/), [IGVFFI8702NWJU](/sequence-files/IGVFFI8702NWJU/), [IGVFFI9850TSIE](/sequence-files/IGVFFI9850TSIE/), [IGVFFI0445HVAM](/sequence-files/IGVFFI0445HVAM/), [IGVFFI6995SPWW](/sequence-files/IGVFFI6995SPWW/) 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/IGVFDS1696YMUM/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1696YMUM](/measurement-sets/IGVFDS1696YMUM/) has sequence file(s): [IGVFFI2690GYIJ](/sequence-files/IGVFFI2690GYIJ/), [IGVFFI8494NBYO](/sequence-files/IGVFFI8494NBYO/), [IGVFFI1443GCTE](/sequence-files/IGVFFI1443GCTE/), [IGVFFI3604KHTE](/sequence-files/IGVFFI3604KHTE/), [IGVFFI8702NWJU](/sequence-files/IGVFFI8702NWJU/), [IGVFFI9850TSIE](/sequence-files/IGVFFI9850TSIE/), [IGVFFI0445HVAM](/sequence-files/IGVFFI0445HVAM/), [IGVFFI6995SPWW](/sequence-files/IGVFFI6995SPWW/) 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/IGVFDS1696YMUM/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing control for",
"detail": "Measurement set [IGVFDS1696YMUM](/measurement-sets/IGVFDS1696YMUM/) 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/IGVFDS1696YMUM/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1696YMUM](/measurement-sets/IGVFDS1696YMUM/) 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/IGVFDS1696YMUM/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS1696YMUM](/measurement-sets/IGVFDS1696YMUM/) 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/IGVFDS1696YMUM/"
}
]
},
"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": "2023-11-30T22:46:23.272078+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/IGVFFI2690GYIJ/",
"accession": "IGVFFI2690GYIJ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:01:31.359940+00:00",
"file_format": "fastq",
"file_size": 3084140,
"href": "/sequence-files/IGVFFI2690GYIJ/@@download/IGVFFI2690GYIJ.fastq.gz",
"md5sum": "6bd058840db200ae01fafb7a3bb82d65",
"s3_uri": "s3://igvf-files/2023/12/05/86959465-92e2-43b6-a214-a08893bc7cb3/IGVFFI2690GYIJ.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-BioRep1-FFRep1-BinAll-PCRrep2_S103_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8494NBYO/",
"accession": "IGVFFI8494NBYO",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:55:11.729238+00:00",
"file_format": "fastq",
"file_size": 3050144,
"href": "/sequence-files/IGVFFI8494NBYO/@@download/IGVFFI8494NBYO.fastq.gz",
"md5sum": "3bc5a4cbc5f4c3d6001cb369fad82e27",
"s3_uri": "s3://igvf-files/2023/12/05/e30dd5f7-fa36-4c20-8b83-0f0ec2b4bb58/IGVFFI8494NBYO.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-BioRep1-FFRep1-BinAll-PCRrep1_S7_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1443GCTE/",
"accession": "IGVFFI1443GCTE",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:29:38.691263+00:00",
"file_format": "fastq",
"file_size": 8932173,
"href": "/sequence-files/IGVFFI1443GCTE/@@download/IGVFFI1443GCTE.fastq.gz",
"md5sum": "c29291a7388b2147ce8943c9c8743902",
"s3_uri": "s3://igvf-files/2023/12/05/0b42feed-b5a4-4765-a07d-ccce2dc9f2ab/IGVFFI1443GCTE.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-BioRep1-FFRep1-BinAll-PCRrep1_S7_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3604KHTE/",
"accession": "IGVFFI3604KHTE",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:42:17.633657+00:00",
"file_format": "fastq",
"file_size": 17452995,
"href": "/sequence-files/IGVFFI3604KHTE/@@download/IGVFFI3604KHTE.fastq.gz",
"md5sum": "0541e8485e0f43d6f1eb000c07c09cb7",
"s3_uri": "s3://igvf-files/2023/12/05/342e6247-e960-4778-960a-83d0ac080b2d/IGVFFI3604KHTE.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-BioRep1-FFRep1-BinAll-PCRrep1_S7_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8702NWJU/",
"accession": "IGVFFI8702NWJU",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:35:58.070649+00:00",
"file_format": "fastq",
"file_size": 8914100,
"href": "/sequence-files/IGVFFI8702NWJU/@@download/IGVFFI8702NWJU.fastq.gz",
"md5sum": "223714006124c80777bb4a966c7fd493",
"s3_uri": "s3://igvf-files/2023/12/05/219c52c4-083b-4ec6-95ba-037459b36a9e/IGVFFI8702NWJU.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-BioRep1-FFRep1-BinAll-PCRrep2_S103_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9850TSIE/",
"accession": "IGVFFI9850TSIE",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:48:42.571155+00:00",
"file_format": "fastq",
"file_size": 18188576,
"href": "/sequence-files/IGVFFI9850TSIE/@@download/IGVFFI9850TSIE.fastq.gz",
"md5sum": "215ae958c3e4dc4a41c1af8305340d20",
"s3_uri": "s3://igvf-files/2023/12/05/0f7ecd0a-b3fe-45ae-8939-5157d9f0e3b3/IGVFFI9850TSIE.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-BioRep1-FFRep1-BinAll-PCRrep2_S103_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0445HVAM/",
"accession": "IGVFFI0445HVAM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:07:38.944422+00:00",
"file_format": "fastq",
"file_size": 2912914,
"href": "/sequence-files/IGVFFI0445HVAM/@@download/IGVFFI0445HVAM.fastq.gz",
"md5sum": "eaa03eda26eb321f332bee40880eef33",
"s3_uri": "s3://igvf-files/2023/12/05/afeef51d-09ca-4126-880a-68a37a342d97/IGVFFI0445HVAM.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-BioRep1-FFRep1-BinAll-PCRrep1_S7_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6995SPWW/",
"accession": "IGVFFI6995SPWW",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:13:48.868380+00:00",
"file_format": "fastq",
"file_size": 2974319,
"href": "/sequence-files/IGVFFI6995SPWW/@@download/IGVFFI6995SPWW.fastq.gz",
"md5sum": "d4bbbc14d83018951b234568f939f470",
"s3_uri": "s3://igvf-files/2023/12/05/e2bd47dc-c8b3-494d-afa5-3dcb76fd9d33/IGVFFI6995SPWW.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-BioRep1-FFRep1-BinAll-PCRrep2_S103_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": "2023-12-20T23:10:21.850875+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1355ITKK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1355ITKK",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-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": "2023-12-05T18:29:38.691263+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "1fed7c53-1513-425c-8533-17ca9a179cac"
}