{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2167TBGK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2167TBGK",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-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 [IGVFDS2167TBGK](/measurement-sets/IGVFDS2167TBGK/) 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/IGVFDS2167TBGK/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2167TBGK](/measurement-sets/IGVFDS2167TBGK/) has sequence file(s) [IGVFFI9600GATJ](/sequence-files/IGVFFI9600GATJ/), [IGVFFI9370SMOO](/sequence-files/IGVFFI9370SMOO/), [IGVFFI8253KHQU](/sequence-files/IGVFFI8253KHQU/), [IGVFFI1604ZAAX](/sequence-files/IGVFFI1604ZAAX/), [IGVFFI6936QCXD](/sequence-files/IGVFFI6936QCXD/), [IGVFFI3778EHOT](/sequence-files/IGVFFI3778EHOT/), [IGVFFI4579CGRK](/sequence-files/IGVFFI4579CGRK/), [IGVFFI6789ZBUG](/sequence-files/IGVFFI6789ZBUG/) 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/IGVFDS2167TBGK/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2167TBGK](/measurement-sets/IGVFDS2167TBGK/) has sequence file(s): [IGVFFI9600GATJ](/sequence-files/IGVFFI9600GATJ/), [IGVFFI9370SMOO](/sequence-files/IGVFFI9370SMOO/), [IGVFFI8253KHQU](/sequence-files/IGVFFI8253KHQU/), [IGVFFI1604ZAAX](/sequence-files/IGVFFI1604ZAAX/), [IGVFFI6936QCXD](/sequence-files/IGVFFI6936QCXD/), [IGVFFI3778EHOT](/sequence-files/IGVFFI3778EHOT/), [IGVFFI4579CGRK](/sequence-files/IGVFFI4579CGRK/), [IGVFFI6789ZBUG](/sequence-files/IGVFFI6789ZBUG/) 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/IGVFDS2167TBGK/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM7075GWHP](/in-vitro-systems/IGVFSM7075GWHP/) 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/IGVFSM7075GWHP/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7075GWHP](/in-vitro-systems/IGVFSM7075GWHP/) 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/IGVFSM7075GWHP/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing control for",
"detail": "Measurement set [IGVFDS2167TBGK](/measurement-sets/IGVFDS2167TBGK/) 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/IGVFDS2167TBGK/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2167TBGK](/measurement-sets/IGVFDS2167TBGK/) 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/IGVFDS2167TBGK/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS2167TBGK](/measurement-sets/IGVFDS2167TBGK/) 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/IGVFDS2167TBGK/"
}
]
},
"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": "2023-11-30T22:46:36.459111+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/IGVFFI9600GATJ/",
"accession": "IGVFFI9600GATJ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:15:51.302029+00:00",
"file_format": "fastq",
"file_size": 2857642,
"href": "/sequence-files/IGVFFI9600GATJ/@@download/IGVFFI9600GATJ.fastq.gz",
"md5sum": "9eda2e27697365b9886edc16a3d137db",
"s3_uri": "s3://igvf-files/2023/12/05/f32a1277-7b67-4040-9d47-e105177c3948/IGVFFI9600GATJ.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-FFRep3-BinAll-PCRrep2_S117_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9370SMOO/",
"accession": "IGVFFI9370SMOO",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:50:50.740575+00:00",
"file_format": "fastq",
"file_size": 16839071,
"href": "/sequence-files/IGVFFI9370SMOO/@@download/IGVFFI9370SMOO.fastq.gz",
"md5sum": "961b93f9fe2715a3b50f9f6f372fc19c",
"s3_uri": "s3://igvf-files/2023/12/05/1e058de1-0a8e-4ae5-b8a3-a0211c53aa02/IGVFFI9370SMOO.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-FFRep3-BinAll-PCRrep2_S117_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8253KHQU/",
"accession": "IGVFFI8253KHQU",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:03:36.175380+00:00",
"file_format": "fastq",
"file_size": 2942322,
"href": "/sequence-files/IGVFFI8253KHQU/@@download/IGVFFI8253KHQU.fastq.gz",
"md5sum": "3ecf144817b8d5bcfd24941138adb24c",
"s3_uri": "s3://igvf-files/2023/12/05/f3bcaf64-6e35-4a37-b4a1-ac54316284de/IGVFFI8253KHQU.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-FFRep3-BinAll-PCRrep2_S117_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1604ZAAX/",
"accession": "IGVFFI1604ZAAX",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:44:26.184306+00:00",
"file_format": "fastq",
"file_size": 16111997,
"href": "/sequence-files/IGVFFI1604ZAAX/@@download/IGVFFI1604ZAAX.fastq.gz",
"md5sum": "7e46446faa934a526d8e82ccaeae7f37",
"s3_uri": "s3://igvf-files/2023/12/05/cd67a9ac-4bd1-4b8c-8b03-a88120bd1c44/IGVFFI1604ZAAX.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-FFRep3-BinAll-PCRrep1_S21_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6936QCXD/",
"accession": "IGVFFI6936QCXD",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:38:03.452455+00:00",
"file_format": "fastq",
"file_size": 8597673,
"href": "/sequence-files/IGVFFI6936QCXD/@@download/IGVFFI6936QCXD.fastq.gz",
"md5sum": "53f644e97f4615b7eae9c255adf475f8",
"s3_uri": "s3://igvf-files/2023/12/05/05996120-ea69-4d57-abb8-e5f06d8d0611/IGVFFI6936QCXD.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-FFRep3-BinAll-PCRrep2_S117_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3778EHOT/",
"accession": "IGVFFI3778EHOT",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:31:48.131164+00:00",
"file_format": "fastq",
"file_size": 8346629,
"href": "/sequence-files/IGVFFI3778EHOT/@@download/IGVFFI3778EHOT.fastq.gz",
"md5sum": "8e3422465c46ce155bc988c42886ce36",
"s3_uri": "s3://igvf-files/2023/12/05/941e0db3-18f3-487b-8df6-5e24a6b3b3fb/IGVFFI3778EHOT.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-FFRep3-BinAll-PCRrep1_S21_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4579CGRK/",
"accession": "IGVFFI4579CGRK",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:57:14.415334+00:00",
"file_format": "fastq",
"file_size": 2858471,
"href": "/sequence-files/IGVFFI4579CGRK/@@download/IGVFFI4579CGRK.fastq.gz",
"md5sum": "6ac2d2121c54d1c43e853e177cad6a01",
"s3_uri": "s3://igvf-files/2023/12/05/c8cfc4dd-4031-439a-9dc1-10f1ee2784bd/IGVFFI4579CGRK.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-FFRep3-BinAll-PCRrep1_S21_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6789ZBUG/",
"accession": "IGVFFI6789ZBUG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:09:40.778758+00:00",
"file_format": "fastq",
"file_size": 2759771,
"href": "/sequence-files/IGVFFI6789ZBUG/@@download/IGVFFI6789ZBUG.fastq.gz",
"md5sum": "54366927262abff55e7b5cd64a8d6e45",
"s3_uri": "s3://igvf-files/2023/12/05/a877138a-3bc3-463e-b152-c7892bb67c7a/IGVFFI6789ZBUG.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-FFRep3-BinAll-PCRrep1_S21_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": "2023-12-20T23:10:49.474737+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7075GWHP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7075GWHP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-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": "2023-12-05T18:31:48.131164+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "d9905b59-3969-474a-b935-6f710ac36798"
}