{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6498KFQL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6498KFQL",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinB_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 [IGVFSM2043RUDS](/in-vitro-systems/IGVFSM2043RUDS/) 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/IGVFSM2043RUDS/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM2043RUDS](/in-vitro-systems/IGVFSM2043RUDS/) 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/IGVFSM2043RUDS/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS6498KFQL](/measurement-sets/IGVFDS6498KFQL/) 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/IGVFDS6498KFQL/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6498KFQL](/measurement-sets/IGVFDS6498KFQL/) has sequence file(s) [IGVFFI0645FTVA](/sequence-files/IGVFFI0645FTVA/), [IGVFFI6713IQGU](/sequence-files/IGVFFI6713IQGU/), [IGVFFI9085QDLY](/sequence-files/IGVFFI9085QDLY/), [IGVFFI7659VEYS](/sequence-files/IGVFFI7659VEYS/), [IGVFFI5665TNPQ](/sequence-files/IGVFFI5665TNPQ/), [IGVFFI2684UNAH](/sequence-files/IGVFFI2684UNAH/), [IGVFFI0052NHLO](/sequence-files/IGVFFI0052NHLO/), [IGVFFI9910KQMC](/sequence-files/IGVFFI9910KQMC/) 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/IGVFDS6498KFQL/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6498KFQL](/measurement-sets/IGVFDS6498KFQL/) has sequence file(s): [IGVFFI0645FTVA](/sequence-files/IGVFFI0645FTVA/), [IGVFFI6713IQGU](/sequence-files/IGVFFI6713IQGU/), [IGVFFI9085QDLY](/sequence-files/IGVFFI9085QDLY/), [IGVFFI7659VEYS](/sequence-files/IGVFFI7659VEYS/), [IGVFFI5665TNPQ](/sequence-files/IGVFFI5665TNPQ/), [IGVFFI2684UNAH](/sequence-files/IGVFFI2684UNAH/), [IGVFFI0052NHLO](/sequence-files/IGVFFI0052NHLO/), [IGVFFI9910KQMC](/sequence-files/IGVFFI9910KQMC/) 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/IGVFDS6498KFQL/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6498KFQL](/measurement-sets/IGVFDS6498KFQL/) 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/IGVFDS6498KFQL/"
}
]
},
"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": "2023-11-30T22:46:16.740288+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/IGVFFI0645FTVA/",
"accession": "IGVFFI0645FTVA",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:28:37.960205+00:00",
"file_format": "fastq",
"file_size": 41708726,
"href": "/sequence-files/IGVFFI0645FTVA/@@download/IGVFFI0645FTVA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ad1876d7-4ea6-4b02-ba47-3809ba083a64/IGVFFI0645FTVA.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-BinB_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6713IQGU/",
"accession": "IGVFFI6713IQGU",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:57:34.707016+00:00",
"file_format": "fastq",
"file_size": 14816229,
"href": "/sequence-files/IGVFFI6713IQGU/@@download/IGVFFI6713IQGU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/42228a7a-d62f-4a5b-880b-626b434c4d01/IGVFFI6713IQGU.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-BinB_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9085QDLY/",
"accession": "IGVFFI9085QDLY",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:03:06.651332+00:00",
"file_format": "fastq",
"file_size": 14141629,
"href": "/sequence-files/IGVFFI9085QDLY/@@download/IGVFFI9085QDLY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/233ca734-4b7a-499e-877d-f4b5b485b04e/IGVFFI9085QDLY.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-BinB_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7659VEYS/",
"accession": "IGVFFI7659VEYS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:08:41.635356+00:00",
"file_format": "fastq",
"file_size": 13283133,
"href": "/sequence-files/IGVFFI7659VEYS/@@download/IGVFFI7659VEYS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/93d6fa69-bd14-45b1-a59e-cf0f0bc6c947/IGVFFI7659VEYS.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-BinB_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5665TNPQ/",
"accession": "IGVFFI5665TNPQ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:46:19.388129+00:00",
"file_format": "fastq",
"file_size": 70827054,
"href": "/sequence-files/IGVFFI5665TNPQ/@@download/IGVFFI5665TNPQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e3887e68-08db-41e7-b6de-23bd183594a6/IGVFFI5665TNPQ.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-BinB_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2684UNAH/",
"accession": "IGVFFI2684UNAH",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:40:17.107340+00:00",
"file_format": "fastq",
"file_size": 75037075,
"href": "/sequence-files/IGVFFI2684UNAH/@@download/IGVFFI2684UNAH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/283de3bd-e1b3-4e9a-b712-7ab9d550a10b/IGVFFI2684UNAH.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-BinB_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0052NHLO/",
"accession": "IGVFFI0052NHLO",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:51:51.385277+00:00",
"file_format": "fastq",
"file_size": 15251570,
"href": "/sequence-files/IGVFFI0052NHLO/@@download/IGVFFI0052NHLO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d36674b7-24e3-49a2-9a3d-3a443fcaee2e/IGVFFI0052NHLO.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-BinB_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9910KQMC/",
"accession": "IGVFFI9910KQMC",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:34:18.324460+00:00",
"file_format": "fastq",
"file_size": 39197230,
"href": "/sequence-files/IGVFFI9910KQMC/@@download/IGVFFI9910KQMC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/beb1bd4f-296e-4383-ac80-d748331315f8/IGVFFI9910KQMC.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-BinB_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": "2023-12-20T23:10:26.831052+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2043RUDS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2043RUDS",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinB"
],
"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 11-20% 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": "2023-12-05T18:28:37.960205+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": "ad74a0fb-7d23-4240-a0a6-0de05dd97a8e"
}