{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3198NALA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3198NALA",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-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 [IGVFSM5557UHMD](/in-vitro-systems/IGVFSM5557UHMD/) 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/IGVFSM5557UHMD/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM5557UHMD](/in-vitro-systems/IGVFSM5557UHMD/) 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/IGVFSM5557UHMD/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS3198NALA](/measurement-sets/IGVFDS3198NALA/) 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/IGVFDS3198NALA/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3198NALA](/measurement-sets/IGVFDS3198NALA/) has sequence file(s) [IGVFFI4862YBMJ](/sequence-files/IGVFFI4862YBMJ/), [IGVFFI5369SCMG](/sequence-files/IGVFFI5369SCMG/), [IGVFFI9047GXNC](/sequence-files/IGVFFI9047GXNC/), [IGVFFI8637BEAM](/sequence-files/IGVFFI8637BEAM/), [IGVFFI3358HAKA](/sequence-files/IGVFFI3358HAKA/), [IGVFFI9693QEGG](/sequence-files/IGVFFI9693QEGG/), [IGVFFI6060VEQO](/sequence-files/IGVFFI6060VEQO/), [IGVFFI8489HAHL](/sequence-files/IGVFFI8489HAHL/) 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/IGVFDS3198NALA/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3198NALA](/measurement-sets/IGVFDS3198NALA/) has sequence file(s): [IGVFFI4862YBMJ](/sequence-files/IGVFFI4862YBMJ/), [IGVFFI5369SCMG](/sequence-files/IGVFFI5369SCMG/), [IGVFFI9047GXNC](/sequence-files/IGVFFI9047GXNC/), [IGVFFI8637BEAM](/sequence-files/IGVFFI8637BEAM/), [IGVFFI3358HAKA](/sequence-files/IGVFFI3358HAKA/), [IGVFFI9693QEGG](/sequence-files/IGVFFI9693QEGG/), [IGVFFI6060VEQO](/sequence-files/IGVFFI6060VEQO/), [IGVFFI8489HAHL](/sequence-files/IGVFFI8489HAHL/) 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/IGVFDS3198NALA/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3198NALA](/measurement-sets/IGVFDS3198NALA/) 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/IGVFDS3198NALA/"
}
]
},
"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": "2023-11-30T22:46:20.461504+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/IGVFFI4862YBMJ/",
"accession": "IGVFFI4862YBMJ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinE-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:58:02.238044+00:00",
"file_format": "fastq",
"file_size": 13510219,
"href": "/sequence-files/IGVFFI4862YBMJ/@@download/IGVFFI4862YBMJ.fastq.gz",
"md5sum": "6a398ea67093fd18c0b98c7d9e3d5295",
"s3_uri": "s3://igvf-files/2023/12/05/2d9d9b3f-a8bc-4d38-a1c5-e59f8e7aed2b/IGVFFI4862YBMJ.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-BinE_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5369SCMG/",
"accession": "IGVFFI5369SCMG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinE-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:52:22.435078+00:00",
"file_format": "fastq",
"file_size": 15354210,
"href": "/sequence-files/IGVFFI5369SCMG/@@download/IGVFFI5369SCMG.fastq.gz",
"md5sum": "be55025a124ad857eac406d856910692",
"s3_uri": "s3://igvf-files/2023/12/05/1aff9e5b-3aed-4907-bcf7-0e5bf7f75946/IGVFFI5369SCMG.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-BinE_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9047GXNC/",
"accession": "IGVFFI9047GXNC",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinE-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:29:06.136402+00:00",
"file_format": "fastq",
"file_size": 41801393,
"href": "/sequence-files/IGVFFI9047GXNC/@@download/IGVFFI9047GXNC.fastq.gz",
"md5sum": "d4224323dc56d2c1f1b3f2af1ae3a142",
"s3_uri": "s3://igvf-files/2023/12/05/bf6a00f9-25c9-4eb0-9f6c-c62c104081cd/IGVFFI9047GXNC.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-BinE_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8637BEAM/",
"accession": "IGVFFI8637BEAM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinE-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:46:48.364557+00:00",
"file_format": "fastq",
"file_size": 66504816,
"href": "/sequence-files/IGVFFI8637BEAM/@@download/IGVFFI8637BEAM.fastq.gz",
"md5sum": "ed2b6f33a86d0924535c2c8d76569eec",
"s3_uri": "s3://igvf-files/2023/12/05/66798715-5cfa-43d0-ab7e-ed4eb385286e/IGVFFI8637BEAM.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-BinE_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3358HAKA/",
"accession": "IGVFFI3358HAKA",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinE-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:34:46.539142+00:00",
"file_format": "fastq",
"file_size": 36885968,
"href": "/sequence-files/IGVFFI3358HAKA/@@download/IGVFFI3358HAKA.fastq.gz",
"md5sum": "b1e169cb296dae838877101673030b24",
"s3_uri": "s3://igvf-files/2023/12/05/6daceab3-7e4d-432f-ab90-5f9466e29b1b/IGVFFI3358HAKA.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-BinE_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9693QEGG/",
"accession": "IGVFFI9693QEGG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:09:09.191563+00:00",
"file_format": "fastq",
"file_size": 12611637,
"href": "/sequence-files/IGVFFI9693QEGG/@@download/IGVFFI9693QEGG.fastq.gz",
"md5sum": "0e0f080af4a87c5039a019b6deb06898",
"s3_uri": "s3://igvf-files/2023/12/05/c07fc766-dff4-48a3-aa46-07bbc6f44ec0/IGVFFI9693QEGG.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-BinE_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6060VEQO/",
"accession": "IGVFFI6060VEQO",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinE-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:03:34.105431+00:00",
"file_format": "fastq",
"file_size": 14332428,
"href": "/sequence-files/IGVFFI6060VEQO/@@download/IGVFFI6060VEQO.fastq.gz",
"md5sum": "2465304c67f1223843b78ddd2a984a5e",
"s3_uri": "s3://igvf-files/2023/12/05/ec566755-f070-403f-aa19-f068b42f56d8/IGVFFI6060VEQO.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-BinE_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8489HAHL/",
"accession": "IGVFFI8489HAHL",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinE-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:40:49.341741+00:00",
"file_format": "fastq",
"file_size": 75393687,
"href": "/sequence-files/IGVFFI8489HAHL/@@download/IGVFFI8489HAHL.fastq.gz",
"md5sum": "510ca4234484dd75ef63bd65413a77df",
"s3_uri": "s3://igvf-files/2023/12/05/c7278bc7-0466-4f6d-a59f-0e39ed7e116d/IGVFFI8489HAHL.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-BinE_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": "2023-12-20T23:09:35.816353+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5557UHMD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5557UHMD",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-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": "2023-12-05T18:29:06.136402+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": "2b2af247-4149-4186-a085-104dc830db2c"
}