{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7365REMW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7365REMW",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-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 [IGVFSM3137EVKW](/in-vitro-systems/IGVFSM3137EVKW/) 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/IGVFSM3137EVKW/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3137EVKW](/in-vitro-systems/IGVFSM3137EVKW/) 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/IGVFSM3137EVKW/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS7365REMW](/measurement-sets/IGVFDS7365REMW/) 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/IGVFDS7365REMW/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7365REMW](/measurement-sets/IGVFDS7365REMW/) has sequence file(s) [IGVFFI8703CHXH](/sequence-files/IGVFFI8703CHXH/), [IGVFFI8126WOAD](/sequence-files/IGVFFI8126WOAD/), [IGVFFI3587AGXB](/sequence-files/IGVFFI3587AGXB/), [IGVFFI2444ZRCB](/sequence-files/IGVFFI2444ZRCB/), [IGVFFI4659RLHB](/sequence-files/IGVFFI4659RLHB/), [IGVFFI2767SEET](/sequence-files/IGVFFI2767SEET/), [IGVFFI6535VGNK](/sequence-files/IGVFFI6535VGNK/), [IGVFFI2868QPVU](/sequence-files/IGVFFI2868QPVU/) 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/IGVFDS7365REMW/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7365REMW](/measurement-sets/IGVFDS7365REMW/) has sequence file(s): [IGVFFI8703CHXH](/sequence-files/IGVFFI8703CHXH/), [IGVFFI8126WOAD](/sequence-files/IGVFFI8126WOAD/), [IGVFFI3587AGXB](/sequence-files/IGVFFI3587AGXB/), [IGVFFI2444ZRCB](/sequence-files/IGVFFI2444ZRCB/), [IGVFFI4659RLHB](/sequence-files/IGVFFI4659RLHB/), [IGVFFI2767SEET](/sequence-files/IGVFFI2767SEET/), [IGVFFI6535VGNK](/sequence-files/IGVFFI6535VGNK/), [IGVFFI2868QPVU](/sequence-files/IGVFFI2868QPVU/) 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/IGVFDS7365REMW/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing control for",
"detail": "Measurement set [IGVFDS7365REMW](/measurement-sets/IGVFDS7365REMW/) 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/IGVFDS7365REMW/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7365REMW](/measurement-sets/IGVFDS7365REMW/) 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/IGVFDS7365REMW/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS7365REMW](/measurement-sets/IGVFDS7365REMW/) 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/IGVFDS7365REMW/"
}
]
},
"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": "2023-11-30T22:46:48.445286+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/IGVFFI8703CHXH/",
"accession": "IGVFFI8703CHXH",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:53:06.513012+00:00",
"file_format": "fastq",
"file_size": 16434054,
"href": "/sequence-files/IGVFFI8703CHXH/@@download/IGVFFI8703CHXH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ccbf1e70-7c8d-49f3-9760-7192011558ec/IGVFFI8703CHXH.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-FFRep2-BinAll-PCRrep2_S131_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8126WOAD/",
"accession": "IGVFFI8126WOAD",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:59:25.277548+00:00",
"file_format": "fastq",
"file_size": 2919825,
"href": "/sequence-files/IGVFFI8126WOAD/@@download/IGVFFI8126WOAD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e9cffeb4-785f-4a76-a270-33f24e18e231/IGVFFI8126WOAD.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-FFRep2-BinAll-PCRrep1_S35_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3587AGXB/",
"accession": "IGVFFI3587AGXB",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:17:53.520075+00:00",
"file_format": "fastq",
"file_size": 2861401,
"href": "/sequence-files/IGVFFI3587AGXB/@@download/IGVFFI3587AGXB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b662f0a5-555d-4a5e-806e-65990e15b42b/IGVFFI3587AGXB.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-FFRep2-BinAll-PCRrep2_S131_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2444ZRCB/",
"accession": "IGVFFI2444ZRCB",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:33:53.565967+00:00",
"file_format": "fastq",
"file_size": 8339033,
"href": "/sequence-files/IGVFFI2444ZRCB/@@download/IGVFFI2444ZRCB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6d872757-9468-4eed-825e-ea2eabb6297b/IGVFFI2444ZRCB.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-FFRep2-BinAll-PCRrep1_S35_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4659RLHB/",
"accession": "IGVFFI4659RLHB",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:40:10.076735+00:00",
"file_format": "fastq",
"file_size": 8505309,
"href": "/sequence-files/IGVFFI4659RLHB/@@download/IGVFFI4659RLHB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/303a0653-fd14-4c25-813e-eb378d423cbe/IGVFFI4659RLHB.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-FFRep2-BinAll-PCRrep2_S131_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2767SEET/",
"accession": "IGVFFI2767SEET",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:11:46.913456+00:00",
"file_format": "fastq",
"file_size": 2735145,
"href": "/sequence-files/IGVFFI2767SEET/@@download/IGVFFI2767SEET.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a2df6dd8-21c8-4e75-bfb8-37f1052e313b/IGVFFI2767SEET.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-FFRep2-BinAll-PCRrep1_S35_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6535VGNK/",
"accession": "IGVFFI6535VGNK",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:05:37.240545+00:00",
"file_format": "fastq",
"file_size": 3056647,
"href": "/sequence-files/IGVFFI6535VGNK/@@download/IGVFFI6535VGNK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8ba703c7-8e81-406f-be78-ff851b8e64eb/IGVFFI6535VGNK.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-FFRep2-BinAll-PCRrep2_S131_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2868QPVU/",
"accession": "IGVFFI2868QPVU",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep2-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:46:34.433487+00:00",
"file_format": "fastq",
"file_size": 15940813,
"href": "/sequence-files/IGVFFI2868QPVU/@@download/IGVFFI2868QPVU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fc13d9f7-c371-499c-805b-249e4b3b0dfc/IGVFFI2868QPVU.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-FFRep2-BinAll-PCRrep1_S35_R2_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": "2023-12-20T23:09:49.330855+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3137EVKW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3137EVKW",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-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": "2023-12-05T18:33:53.565967+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "e78f7974-6cbb-45f6-9f23-a25d61bfece4"
}