{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7205UOTV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7205UOTV",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input_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 [IGVFSM8384KCKA](/in-vitro-systems/IGVFSM8384KCKA/) 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/IGVFSM8384KCKA/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM8384KCKA](/in-vitro-systems/IGVFSM8384KCKA/) 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/IGVFSM8384KCKA/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS7205UOTV](/measurement-sets/IGVFDS7205UOTV/) 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/IGVFDS7205UOTV/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7205UOTV](/measurement-sets/IGVFDS7205UOTV/) has sequence file(s) [IGVFFI6359EZAI](/sequence-files/IGVFFI6359EZAI/), [IGVFFI9519XNGP](/sequence-files/IGVFFI9519XNGP/), [IGVFFI1582BKUC](/sequence-files/IGVFFI1582BKUC/), [IGVFFI9778XHVB](/sequence-files/IGVFFI9778XHVB/), [IGVFFI6783OLIG](/sequence-files/IGVFFI6783OLIG/), [IGVFFI1286GWLQ](/sequence-files/IGVFFI1286GWLQ/), [IGVFFI5504WJZH](/sequence-files/IGVFFI5504WJZH/), [IGVFFI6381GHIK](/sequence-files/IGVFFI6381GHIK/) 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/IGVFDS7205UOTV/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7205UOTV](/measurement-sets/IGVFDS7205UOTV/) has sequence file(s): [IGVFFI6359EZAI](/sequence-files/IGVFFI6359EZAI/), [IGVFFI9519XNGP](/sequence-files/IGVFFI9519XNGP/), [IGVFFI1582BKUC](/sequence-files/IGVFFI1582BKUC/), [IGVFFI9778XHVB](/sequence-files/IGVFFI9778XHVB/), [IGVFFI6783OLIG](/sequence-files/IGVFFI6783OLIG/), [IGVFFI1286GWLQ](/sequence-files/IGVFFI1286GWLQ/), [IGVFFI5504WJZH](/sequence-files/IGVFFI5504WJZH/), [IGVFFI6381GHIK](/sequence-files/IGVFFI6381GHIK/) 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/IGVFDS7205UOTV/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing control for",
"detail": "Measurement set [IGVFDS7205UOTV](/measurement-sets/IGVFDS7205UOTV/) has no `control_for`. The `control_file_sets` should be patched on the file sets it serves as a control for and this property, `control_for`, will be reverse calculated. File sets that specify a control type are expected to be a control for other file sets.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_control_for_control_type",
"path": "/measurement-sets/IGVFDS7205UOTV/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7205UOTV](/measurement-sets/IGVFDS7205UOTV/) 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/IGVFDS7205UOTV/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS7205UOTV](/measurement-sets/IGVFDS7205UOTV/) has no `targeted_genes`. ChIP-seq and CRISPR flow cytometry assays are expected to specify targeted gene(s).",
"level": 40,
"level_name": "WARNING",
"name": "audit_targeted_genes",
"path": "/measurement-sets/IGVFDS7205UOTV/"
}
]
},
"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": [],
"control_type": "unsorted FACS input",
"creation_timestamp": "2023-11-30T22:46:15.685090+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/IGVFFI6359EZAI/",
"accession": "IGVFFI6359EZAI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:03:52.337502+00:00",
"file_format": "fastq",
"file_size": 13956918,
"href": "/sequence-files/IGVFFI6359EZAI/@@download/IGVFFI6359EZAI.fastq.gz",
"md5sum": "7c7a1f48f75ce42401414c2a1f29b8c9",
"s3_uri": "s3://igvf-files/2023/12/05/4b8f5d3f-1bc6-4f27-ab7c-5fcf30393415/IGVFFI6359EZAI.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-BinAll_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9519XNGP/",
"accession": "IGVFFI9519XNGP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:47:07.248814+00:00",
"file_format": "fastq",
"file_size": 71675904,
"href": "/sequence-files/IGVFFI9519XNGP/@@download/IGVFFI9519XNGP.fastq.gz",
"md5sum": "11ae9a40ffa1f753d0422c1a5068dffc",
"s3_uri": "s3://igvf-files/2023/12/05/a8d4d7c0-6bf3-448d-9b88-a69ab7744c8d/IGVFFI9519XNGP.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-BinAll_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1582BKUC/",
"accession": "IGVFFI1582BKUC",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:58:20.758212+00:00",
"file_format": "fastq",
"file_size": 14353684,
"href": "/sequence-files/IGVFFI1582BKUC/@@download/IGVFFI1582BKUC.fastq.gz",
"md5sum": "e5ab8637056f5c5e25d9d588b9ba2eca",
"s3_uri": "s3://igvf-files/2023/12/05/fafd7d4d-f75e-46f8-8e58-8f1eed49174d/IGVFFI1582BKUC.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-BinAll_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9778XHVB/",
"accession": "IGVFFI9778XHVB",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:35:05.131547+00:00",
"file_format": "fastq",
"file_size": 40166920,
"href": "/sequence-files/IGVFFI9778XHVB/@@download/IGVFFI9778XHVB.fastq.gz",
"md5sum": "dea743358cce505eb4383b45a168750a",
"s3_uri": "s3://igvf-files/2023/12/05/c2715eb5-d977-4ea6-a3a9-4bdf56ecdd66/IGVFFI9778XHVB.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-BinAll_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6783OLIG/",
"accession": "IGVFFI6783OLIG",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:29:24.668802+00:00",
"file_format": "fastq",
"file_size": 41686391,
"href": "/sequence-files/IGVFFI6783OLIG/@@download/IGVFFI6783OLIG.fastq.gz",
"md5sum": "29de9260207cd343133bfa78176d131e",
"s3_uri": "s3://igvf-files/2023/12/05/64310963-314c-4e89-9b9b-909d69c62cfd/IGVFFI6783OLIG.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-BinAll_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1286GWLQ/",
"accession": "IGVFFI1286GWLQ",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:41:09.294422+00:00",
"file_format": "fastq",
"file_size": 74647597,
"href": "/sequence-files/IGVFFI1286GWLQ/@@download/IGVFFI1286GWLQ.fastq.gz",
"md5sum": "3f6aeb6ad9c81c9feb4c928a8094122c",
"s3_uri": "s3://igvf-files/2023/12/05/105a825b-dbbf-458e-b270-ed9aee6ab882/IGVFFI1286GWLQ.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-BinAll_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5504WJZH/",
"accession": "IGVFFI5504WJZH",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:09:27.709021+00:00",
"file_format": "fastq",
"file_size": 13401687,
"href": "/sequence-files/IGVFFI5504WJZH/@@download/IGVFFI5504WJZH.fastq.gz",
"md5sum": "da1b8aae00b0b17515a4122a49b1b434",
"s3_uri": "s3://igvf-files/2023/12/05/ff2a639a-330b-4784-81f8-c9b4f8d5312c/IGVFFI5504WJZH.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-BinAll_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6381GHIK/",
"accession": "IGVFFI6381GHIK",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:52:40.796951+00:00",
"file_format": "fastq",
"file_size": 15165181,
"href": "/sequence-files/IGVFFI6381GHIK/@@download/IGVFFI6381GHIK.fastq.gz",
"md5sum": "82bbae15401a37622e3e12276c92dc28",
"s3_uri": "s3://igvf-files/2023/12/05/dd7dd0d6-4778-4cb9-a9a8-b692483f8e4d/IGVFFI6381GHIK.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-BinAll_I1_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": "2023-12-20T23:11:02.173880+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8384KCKA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8384KCKA",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-FACS_Input"
],
"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 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": "2023-12-05T18:29:24.668802+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "68c30b80-e74b-4c24-8813-2a0a750d59e8"
}