{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9005ISSR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9005ISSR",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-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 [IGVFSM2582ALNT](/in-vitro-systems/IGVFSM2582ALNT/) 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/IGVFSM2582ALNT/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM2582ALNT](/in-vitro-systems/IGVFSM2582ALNT/) 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/IGVFSM2582ALNT/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9005ISSR](/measurement-sets/IGVFDS9005ISSR/) 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/IGVFDS9005ISSR/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9005ISSR](/measurement-sets/IGVFDS9005ISSR/) has sequence file(s) [IGVFFI4322LYOJ](/sequence-files/IGVFFI4322LYOJ/), [IGVFFI7242IWAI](/sequence-files/IGVFFI7242IWAI/), [IGVFFI2860SNQR](/sequence-files/IGVFFI2860SNQR/), [IGVFFI7553AHEM](/sequence-files/IGVFFI7553AHEM/), [IGVFFI3231KAKC](/sequence-files/IGVFFI3231KAKC/), [IGVFFI6508PDMY](/sequence-files/IGVFFI6508PDMY/), [IGVFFI0429NEMU](/sequence-files/IGVFFI0429NEMU/), [IGVFFI7391OVWA](/sequence-files/IGVFFI7391OVWA/) 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/IGVFDS9005ISSR/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9005ISSR](/measurement-sets/IGVFDS9005ISSR/) has sequence file(s): [IGVFFI4322LYOJ](/sequence-files/IGVFFI4322LYOJ/), [IGVFFI7242IWAI](/sequence-files/IGVFFI7242IWAI/), [IGVFFI2860SNQR](/sequence-files/IGVFFI2860SNQR/), [IGVFFI7553AHEM](/sequence-files/IGVFFI7553AHEM/), [IGVFFI3231KAKC](/sequence-files/IGVFFI3231KAKC/), [IGVFFI6508PDMY](/sequence-files/IGVFFI6508PDMY/), [IGVFFI0429NEMU](/sequence-files/IGVFFI0429NEMU/), [IGVFFI7391OVWA](/sequence-files/IGVFFI7391OVWA/) 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/IGVFDS9005ISSR/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9005ISSR](/measurement-sets/IGVFDS9005ISSR/) 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/IGVFDS9005ISSR/"
}
]
},
"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": "2023-11-30T22:46:40.109878+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/IGVFFI4322LYOJ/",
"accession": "IGVFFI4322LYOJ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinE-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:56:57.143300+00:00",
"file_format": "fastq",
"file_size": 2786807,
"href": "/sequence-files/IGVFFI4322LYOJ/@@download/IGVFFI4322LYOJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/815fcf1c-c39e-40cf-84ff-9cb5f365aa1d/IGVFFI4322LYOJ.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-BioRep1-FFRep3-BinE-PCRrep1_S19_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7242IWAI/",
"accession": "IGVFFI7242IWAI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:15:33.973670+00:00",
"file_format": "fastq",
"file_size": 2721637,
"href": "/sequence-files/IGVFFI7242IWAI/@@download/IGVFFI7242IWAI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1ca2eda3-775b-431f-bc2e-3be28777bd03/IGVFFI7242IWAI.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-BioRep1-FFRep3-BinE-PCRrep2_S115_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2860SNQR/",
"accession": "IGVFFI2860SNQR",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinE-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:03:18.866944+00:00",
"file_format": "fastq",
"file_size": 2831463,
"href": "/sequence-files/IGVFFI2860SNQR/@@download/IGVFFI2860SNQR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/dddd2c8c-dd44-40fe-aeb3-ecfafb1c4340/IGVFFI2860SNQR.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-BioRep1-FFRep3-BinE-PCRrep2_S115_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7553AHEM/",
"accession": "IGVFFI7553AHEM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinE-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:09:23.315090+00:00",
"file_format": "fastq",
"file_size": 2662212,
"href": "/sequence-files/IGVFFI7553AHEM/@@download/IGVFFI7553AHEM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/427741ff-f343-4efb-90b1-1d1e44cf7b20/IGVFFI7553AHEM.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-BioRep1-FFRep3-BinE-PCRrep1_S19_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3231KAKC/",
"accession": "IGVFFI3231KAKC",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinE-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:31:26.663354+00:00",
"file_format": "fastq",
"file_size": 7861593,
"href": "/sequence-files/IGVFFI3231KAKC/@@download/IGVFFI3231KAKC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/accdb26e-1ddc-437d-843f-b44bdad51861/IGVFFI3231KAKC.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-BioRep1-FFRep3-BinE-PCRrep1_S19_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6508PDMY/",
"accession": "IGVFFI6508PDMY",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinE-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:44:07.899752+00:00",
"file_format": "fastq",
"file_size": 15284323,
"href": "/sequence-files/IGVFFI6508PDMY/@@download/IGVFFI6508PDMY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6c071145-77ee-4c2f-b56d-5d774260ea9b/IGVFFI6508PDMY.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-BioRep1-FFRep3-BinE-PCRrep1_S19_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0429NEMU/",
"accession": "IGVFFI0429NEMU",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinE-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:37:45.935123+00:00",
"file_format": "fastq",
"file_size": 7900531,
"href": "/sequence-files/IGVFFI0429NEMU/@@download/IGVFFI0429NEMU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/55220a22-db3e-4d00-b3ff-af4ab73d31ce/IGVFFI0429NEMU.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-BioRep1-FFRep3-BinE-PCRrep2_S115_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7391OVWA/",
"accession": "IGVFFI7391OVWA",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinE-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:50:32.604040+00:00",
"file_format": "fastq",
"file_size": 15703787,
"href": "/sequence-files/IGVFFI7391OVWA/@@download/IGVFFI7391OVWA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/73877aaa-ead9-4154-8d48-0002de9bcab7/IGVFFI7391OVWA.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-BioRep1-FFRep3-BinE-PCRrep2_S115_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": "2023-12-20T23:09:59.168979+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2582ALNT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2582ALNT",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-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": "2023-12-05T18:31:26.663354+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": "b35168d2-a901-4a01-b367-7f3368042ff3"
}