{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7093IAOE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7093IAOE",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-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 [IGVFSM1683BAMH](/in-vitro-systems/IGVFSM1683BAMH/) 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/IGVFSM1683BAMH/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1683BAMH](/in-vitro-systems/IGVFSM1683BAMH/) 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/IGVFSM1683BAMH/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS7093IAOE](/measurement-sets/IGVFDS7093IAOE/) 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/IGVFDS7093IAOE/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7093IAOE](/measurement-sets/IGVFDS7093IAOE/) has sequence file(s) [IGVFFI9992APID](/sequence-files/IGVFFI9992APID/), [IGVFFI4543CCXP](/sequence-files/IGVFFI4543CCXP/), [IGVFFI7929KKKP](/sequence-files/IGVFFI7929KKKP/), [IGVFFI1037AVDU](/sequence-files/IGVFFI1037AVDU/), [IGVFFI9586IXGV](/sequence-files/IGVFFI9586IXGV/), [IGVFFI6054STOB](/sequence-files/IGVFFI6054STOB/), [IGVFFI7938FGMG](/sequence-files/IGVFFI7938FGMG/), [IGVFFI1886RZCQ](/sequence-files/IGVFFI1886RZCQ/) 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/IGVFDS7093IAOE/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7093IAOE](/measurement-sets/IGVFDS7093IAOE/) has sequence file(s): [IGVFFI9992APID](/sequence-files/IGVFFI9992APID/), [IGVFFI4543CCXP](/sequence-files/IGVFFI4543CCXP/), [IGVFFI7929KKKP](/sequence-files/IGVFFI7929KKKP/), [IGVFFI1037AVDU](/sequence-files/IGVFFI1037AVDU/), [IGVFFI9586IXGV](/sequence-files/IGVFFI9586IXGV/), [IGVFFI6054STOB](/sequence-files/IGVFFI6054STOB/), [IGVFFI7938FGMG](/sequence-files/IGVFFI7938FGMG/), [IGVFFI1886RZCQ](/sequence-files/IGVFFI1886RZCQ/) 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/IGVFDS7093IAOE/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7093IAOE](/measurement-sets/IGVFDS7093IAOE/) 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/IGVFDS7093IAOE/"
}
]
},
"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": "2023-12-01T00:01:43.981904+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/IGVFFI9992APID/",
"accession": "IGVFFI9992APID",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinB-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:04:19.953990+00:00",
"file_format": "fastq",
"file_size": 14368638,
"href": "/sequence-files/IGVFFI9992APID/@@download/IGVFFI9992APID.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/624ca626-2c8b-4a4c-a492-01aa818cc49b/IGVFFI9992APID.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-2-BinB_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4543CCXP/",
"accession": "IGVFFI4543CCXP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinB-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:53:08.400747+00:00",
"file_format": "fastq",
"file_size": 15913125,
"href": "/sequence-files/IGVFFI4543CCXP/@@download/IGVFFI4543CCXP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c0bb3fce-ef3e-4a6b-9e78-1948749831aa/IGVFFI4543CCXP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-2-BinB_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7929KKKP/",
"accession": "IGVFFI7929KKKP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinB-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:35:32.962744+00:00",
"file_format": "fastq",
"file_size": 79524114,
"href": "/sequence-files/IGVFFI7929KKKP/@@download/IGVFFI7929KKKP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/441925e7-380f-4220-919d-fb16ebb62556/IGVFFI7929KKKP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-1-BinB_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1037AVDU/",
"accession": "IGVFFI1037AVDU",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinB-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:24:07.945668+00:00",
"file_format": "fastq",
"file_size": 44232454,
"href": "/sequence-files/IGVFFI1037AVDU/@@download/IGVFFI1037AVDU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b83ee281-7dd5-44b8-8a79-5d5ffd5f6af4/IGVFFI1037AVDU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-1-BinB_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9586IXGV/",
"accession": "IGVFFI9586IXGV",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinB-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:41:38.236357+00:00",
"file_format": "fastq",
"file_size": 76712164,
"href": "/sequence-files/IGVFFI9586IXGV/@@download/IGVFFI9586IXGV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/997830f7-ea12-4ca8-bf5c-b01c697f35af/IGVFFI9586IXGV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-2-BinB_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6054STOB/",
"accession": "IGVFFI6054STOB",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinB-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:47:35.278903+00:00",
"file_format": "fastq",
"file_size": 16217433,
"href": "/sequence-files/IGVFFI6054STOB/@@download/IGVFFI6054STOB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8ec38a06-bec8-4303-8a0e-775dded90b03/IGVFFI6054STOB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-1-BinB_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7938FGMG/",
"accession": "IGVFFI7938FGMG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinB-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:58:48.211253+00:00",
"file_format": "fastq",
"file_size": 14868405,
"href": "/sequence-files/IGVFFI7938FGMG/@@download/IGVFFI7938FGMG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4e1138f6-7dd0-416d-80a8-acebe298bc97/IGVFFI7938FGMG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-1-BinB_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1886RZCQ/",
"accession": "IGVFFI1886RZCQ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-BinB-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:29:52.428024+00:00",
"file_format": "fastq",
"file_size": 42879272,
"href": "/sequence-files/IGVFFI1886RZCQ/@@download/IGVFFI1886RZCQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/cc084580-3cd9-4c74-9cef-f1bc05116f33/IGVFFI1886RZCQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-2-D21-pPPIF-Amp-pPPIF-1-1-2-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": "2023-12-20T23:10:42.078843+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1683BAMH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1683BAMH",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep1-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": "2023-12-05T18:24:07.945668+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": "d3c55410-47d1-4975-870f-f3bead5fbb66"
}