{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5585HGSK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5585HGSK",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep3-BinE_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 [IGVFSM1388TFMJ](/in-vitro-systems/IGVFSM1388TFMJ/) 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/IGVFSM1388TFMJ/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1388TFMJ](/in-vitro-systems/IGVFSM1388TFMJ/) 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/IGVFSM1388TFMJ/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS5585HGSK](/measurement-sets/IGVFDS5585HGSK/) 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/IGVFDS5585HGSK/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5585HGSK](/measurement-sets/IGVFDS5585HGSK/) has sequence file(s) [IGVFFI8083QXLK](/sequence-files/IGVFFI8083QXLK/), [IGVFFI8953YZHJ](/sequence-files/IGVFFI8953YZHJ/), [IGVFFI5673DNYD](/sequence-files/IGVFFI5673DNYD/), [IGVFFI7085VKTZ](/sequence-files/IGVFFI7085VKTZ/), [IGVFFI5439GJFZ](/sequence-files/IGVFFI5439GJFZ/), [IGVFFI4575GHXT](/sequence-files/IGVFFI4575GHXT/), [IGVFFI5067YCFP](/sequence-files/IGVFFI5067YCFP/), [IGVFFI3726GIXG](/sequence-files/IGVFFI3726GIXG/) 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/IGVFDS5585HGSK/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5585HGSK](/measurement-sets/IGVFDS5585HGSK/) has sequence file(s): [IGVFFI8083QXLK](/sequence-files/IGVFFI8083QXLK/), [IGVFFI8953YZHJ](/sequence-files/IGVFFI8953YZHJ/), [IGVFFI5673DNYD](/sequence-files/IGVFFI5673DNYD/), [IGVFFI7085VKTZ](/sequence-files/IGVFFI7085VKTZ/), [IGVFFI5439GJFZ](/sequence-files/IGVFFI5439GJFZ/), [IGVFFI4575GHXT](/sequence-files/IGVFFI4575GHXT/), [IGVFFI5067YCFP](/sequence-files/IGVFFI5067YCFP/), [IGVFFI3726GIXG](/sequence-files/IGVFFI3726GIXG/) 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/IGVFDS5585HGSK/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5585HGSK](/measurement-sets/IGVFDS5585HGSK/) 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/IGVFDS5585HGSK/"
}
]
},
"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": "2023-11-30T22:46:58.645361+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/IGVFFI8083QXLK/",
"accession": "IGVFFI8083QXLK",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep3-BinE-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:00:08.740687+00:00",
"file_format": "fastq",
"file_size": 2818515,
"href": "/sequence-files/IGVFFI8083QXLK/@@download/IGVFFI8083QXLK.fastq.gz",
"md5sum": "a7de83a9bc0a1a11a0ab09a04594bf3a",
"s3_uri": "s3://igvf-files/2023/12/05/f3ba6440-4d34-4aac-bd8a-cb172744726b/IGVFFI8083QXLK.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-FFRep3-BinE-PCRrep1_S40_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8953YZHJ/",
"accession": "IGVFFI8953YZHJ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep3-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:18:41.203848+00:00",
"file_format": "fastq",
"file_size": 2846131,
"href": "/sequence-files/IGVFFI8953YZHJ/@@download/IGVFFI8953YZHJ.fastq.gz",
"md5sum": "fa33137dea9e9b904720b3edb5aee41c",
"s3_uri": "s3://igvf-files/2023/12/05/7884952e-6bc4-477b-a5e6-668f1c7984fb/IGVFFI8953YZHJ.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-FFRep3-BinE-PCRrep2_S136_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5673DNYD/",
"accession": "IGVFFI5673DNYD",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep3-BinE-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:12:30.470120+00:00",
"file_format": "fastq",
"file_size": 2738764,
"href": "/sequence-files/IGVFFI5673DNYD/@@download/IGVFFI5673DNYD.fastq.gz",
"md5sum": "a37441869759cd3e49292ec235a06109",
"s3_uri": "s3://igvf-files/2023/12/05/a0433c37-18c5-4e41-a202-14caec3eea7d/IGVFFI5673DNYD.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-FFRep3-BinE-PCRrep1_S40_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7085VKTZ/",
"accession": "IGVFFI7085VKTZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep3-BinE-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:34:38.463212+00:00",
"file_format": "fastq",
"file_size": 8131666,
"href": "/sequence-files/IGVFFI7085VKTZ/@@download/IGVFFI7085VKTZ.fastq.gz",
"md5sum": "f5bd12d3b761b92fda745b355929ab8a",
"s3_uri": "s3://igvf-files/2023/12/05/dd5d93dc-8c47-4f65-8906-1763d208b0ae/IGVFFI7085VKTZ.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-FFRep3-BinE-PCRrep1_S40_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5439GJFZ/",
"accession": "IGVFFI5439GJFZ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep3-BinE-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:06:21.048288+00:00",
"file_format": "fastq",
"file_size": 2898427,
"href": "/sequence-files/IGVFFI5439GJFZ/@@download/IGVFFI5439GJFZ.fastq.gz",
"md5sum": "720d87cc681cdb90a9405dbe7345029e",
"s3_uri": "s3://igvf-files/2023/12/05/af1200bd-7f9b-4188-a7db-4ece6db3524b/IGVFFI5439GJFZ.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-FFRep3-BinE-PCRrep2_S136_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4575GHXT/",
"accession": "IGVFFI4575GHXT",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep3-BinE-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:40:55.854202+00:00",
"file_format": "fastq",
"file_size": 8310692,
"href": "/sequence-files/IGVFFI4575GHXT/@@download/IGVFFI4575GHXT.fastq.gz",
"md5sum": "23c83f8b2716a0e189ede780c9b122eb",
"s3_uri": "s3://igvf-files/2023/12/05/95e33304-876c-493c-b0fa-67d602e0c3cf/IGVFFI4575GHXT.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-FFRep3-BinE-PCRrep2_S136_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5067YCFP/",
"accession": "IGVFFI5067YCFP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep3-BinE-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:47:20.356374+00:00",
"file_format": "fastq",
"file_size": 15921122,
"href": "/sequence-files/IGVFFI5067YCFP/@@download/IGVFFI5067YCFP.fastq.gz",
"md5sum": "8c77163da6c4ef17caf9984758935644",
"s3_uri": "s3://igvf-files/2023/12/05/b502ae88-3e39-43c1-be54-c735baff15f8/IGVFFI5067YCFP.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-FFRep3-BinE-PCRrep1_S40_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3726GIXG/",
"accession": "IGVFFI3726GIXG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep3-BinE-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:53:51.958297+00:00",
"file_format": "fastq",
"file_size": 16825434,
"href": "/sequence-files/IGVFFI3726GIXG/@@download/IGVFFI3726GIXG.fastq.gz",
"md5sum": "8284e4dd34a3a2d1ddf6aa7778d9437b",
"s3_uri": "s3://igvf-files/2023/12/05/bb7bc39f-f1cf-402a-b4d0-032e280a5f50/IGVFFI3726GIXG.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-FFRep3-BinE-PCRrep2_S136_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": "2023-12-20T23:11:13.685725+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1388TFMJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1388TFMJ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep4-FFrep3-BinE"
],
"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 80-90% 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": "2023-12-05T18:34:38.463212+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": "7493b139-139a-4039-841a-57fa765fd6ee"
}