{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5416ECKJ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5416ECKJ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinC_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 [IGVFSM8470FMQN](/in-vitro-systems/IGVFSM8470FMQN/) 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/IGVFSM8470FMQN/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM8470FMQN](/in-vitro-systems/IGVFSM8470FMQN/) 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/IGVFSM8470FMQN/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS5416ECKJ](/measurement-sets/IGVFDS5416ECKJ/) 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/IGVFDS5416ECKJ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5416ECKJ](/measurement-sets/IGVFDS5416ECKJ/) has sequence file(s) [IGVFFI1440QZIF](/sequence-files/IGVFFI1440QZIF/), [IGVFFI8519BPYB](/sequence-files/IGVFFI8519BPYB/), [IGVFFI2386NBNW](/sequence-files/IGVFFI2386NBNW/), [IGVFFI6806MHWJ](/sequence-files/IGVFFI6806MHWJ/), [IGVFFI5595KJJE](/sequence-files/IGVFFI5595KJJE/), [IGVFFI0230PQCC](/sequence-files/IGVFFI0230PQCC/), [IGVFFI6767GLGN](/sequence-files/IGVFFI6767GLGN/), [IGVFFI3977VKWA](/sequence-files/IGVFFI3977VKWA/) 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/IGVFDS5416ECKJ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5416ECKJ](/measurement-sets/IGVFDS5416ECKJ/) has sequence file(s): [IGVFFI1440QZIF](/sequence-files/IGVFFI1440QZIF/), [IGVFFI8519BPYB](/sequence-files/IGVFFI8519BPYB/), [IGVFFI2386NBNW](/sequence-files/IGVFFI2386NBNW/), [IGVFFI6806MHWJ](/sequence-files/IGVFFI6806MHWJ/), [IGVFFI5595KJJE](/sequence-files/IGVFFI5595KJJE/), [IGVFFI0230PQCC](/sequence-files/IGVFFI0230PQCC/), [IGVFFI6767GLGN](/sequence-files/IGVFFI6767GLGN/), [IGVFFI3977VKWA](/sequence-files/IGVFFI3977VKWA/) 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/IGVFDS5416ECKJ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5416ECKJ](/measurement-sets/IGVFDS5416ECKJ/) 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/IGVFDS5416ECKJ/"
}
]
},
"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": [],
"creation_timestamp": "2023-11-30T22:46:18.365476+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/IGVFFI1440QZIF/",
"accession": "IGVFFI1440QZIF",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:40:26.639959+00:00",
"file_format": "fastq",
"file_size": 76677437,
"href": "/sequence-files/IGVFFI1440QZIF/@@download/IGVFFI1440QZIF.fastq.gz",
"md5sum": "ed9f5194f459e44beac72f2b360032a0",
"s3_uri": "s3://igvf-files/2023/12/05/32fc5138-c4b1-4c06-bc83-a6e17c611429/IGVFFI1440QZIF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-8-D21-pPPIF-Amp-pPPIF-2-2-1-BinC_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8519BPYB/",
"accession": "IGVFFI8519BPYB",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:08:50.817234+00:00",
"file_format": "fastq",
"file_size": 14303327,
"href": "/sequence-files/IGVFFI8519BPYB/@@download/IGVFFI8519BPYB.fastq.gz",
"md5sum": "0aff771e3fcd1c8f9f7a7caee03880b3",
"s3_uri": "s3://igvf-files/2023/12/05/b6a7f971-f20a-4484-a894-af51b4c1e0ce/IGVFFI8519BPYB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-8-D21-pPPIF-Amp-pPPIF-2-2-2-BinC_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2386NBNW/",
"accession": "IGVFFI2386NBNW",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:57:43.928368+00:00",
"file_format": "fastq",
"file_size": 15316167,
"href": "/sequence-files/IGVFFI2386NBNW/@@download/IGVFFI2386NBNW.fastq.gz",
"md5sum": "570bf80935bf1a064f8ab1d686520bbd",
"s3_uri": "s3://igvf-files/2023/12/05/4c1239a4-0673-468e-93a1-8715b1199cb1/IGVFFI2386NBNW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-8-D21-pPPIF-Amp-pPPIF-2-2-2-BinC_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6806MHWJ/",
"accession": "IGVFFI6806MHWJ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:28:47.173798+00:00",
"file_format": "fastq",
"file_size": 42784607,
"href": "/sequence-files/IGVFFI6806MHWJ/@@download/IGVFFI6806MHWJ.fastq.gz",
"md5sum": "5ba341715075fb098bd35435e1954e30",
"s3_uri": "s3://igvf-files/2023/12/05/e69a2ada-d00e-4725-93eb-96be4d80119b/IGVFFI6806MHWJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-8-D21-pPPIF-Amp-pPPIF-2-2-1-BinC_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5595KJJE/",
"accession": "IGVFFI5595KJJE",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:52:00.468140+00:00",
"file_format": "fastq",
"file_size": 15539554,
"href": "/sequence-files/IGVFFI5595KJJE/@@download/IGVFFI5595KJJE.fastq.gz",
"md5sum": "12aad78b95026fb0014a99cfab1946c5",
"s3_uri": "s3://igvf-files/2023/12/05/7d02e8ef-1637-4361-9169-9841a01b61c9/IGVFFI5595KJJE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-8-D21-pPPIF-Amp-pPPIF-2-2-1-BinC_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0230PQCC/",
"accession": "IGVFFI0230PQCC",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:46:28.913724+00:00",
"file_format": "fastq",
"file_size": 75774723,
"href": "/sequence-files/IGVFFI0230PQCC/@@download/IGVFFI0230PQCC.fastq.gz",
"md5sum": "d2a0e967caf8bbc2568bc5c52d4911e9",
"s3_uri": "s3://igvf-files/2023/12/05/186a5e0b-92ad-4407-911c-85ef01a94e6f/IGVFFI0230PQCC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-8-D21-pPPIF-Amp-pPPIF-2-2-2-BinC_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6767GLGN/",
"accession": "IGVFFI6767GLGN",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:03:15.756731+00:00",
"file_format": "fastq",
"file_size": 14443248,
"href": "/sequence-files/IGVFFI6767GLGN/@@download/IGVFFI6767GLGN.fastq.gz",
"md5sum": "7ae5896a860909e8d1af99c18e31716e",
"s3_uri": "s3://igvf-files/2023/12/05/451bc0f7-8262-482b-8b29-25896ed57c12/IGVFFI6767GLGN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-8-D21-pPPIF-Amp-pPPIF-2-2-1-BinC_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3977VKWA/",
"accession": "IGVFFI3977VKWA",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:34:27.518431+00:00",
"file_format": "fastq",
"file_size": 42186443,
"href": "/sequence-files/IGVFFI3977VKWA/@@download/IGVFFI3977VKWA.fastq.gz",
"md5sum": "07d7bc5dc8e2afa68ba6a13f83c0c4e3",
"s3_uri": "s3://igvf-files/2023/12/05/4f5d04b9-13f5-465c-b28a-57c05d5584d3/IGVFFI3977VKWA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-8-D21-pPPIF-Amp-pPPIF-2-2-2-BinC_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": "2023-12-20T23:10:50.909720+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8470FMQN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8470FMQN",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinC"
],
"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 (sorting details: FACS bin for 35-45% expression of PPIF) 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": "2023-12-05T18:28:47.173798+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"status": "released",
"symbol": "PPIF",
"synonyms": [
"PPIase F",
"peptidylprolyl isomerase F",
"Cyp-D",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIF",
"CyP-M",
"cyclophilin F",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"cyclophilin 3",
"cyclophilin D",
"rotamase F",
"mitochondrial cyclophilin",
"CypD",
"CYP3"
]
}
],
"uuid": "963a3a62-a597-41fa-8757-351069fcb947"
}