{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7400NQET/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7400NQET",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-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 [IGVFSM9690YXEE](/in-vitro-systems/IGVFSM9690YXEE/) 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/IGVFSM9690YXEE/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM9690YXEE](/in-vitro-systems/IGVFSM9690YXEE/) 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/IGVFSM9690YXEE/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS7400NQET](/measurement-sets/IGVFDS7400NQET/) 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/IGVFDS7400NQET/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7400NQET](/measurement-sets/IGVFDS7400NQET/) has sequence file(s) [IGVFFI7288ZSLY](/sequence-files/IGVFFI7288ZSLY/), [IGVFFI5292DWTM](/sequence-files/IGVFFI5292DWTM/), [IGVFFI6153OKOT](/sequence-files/IGVFFI6153OKOT/), [IGVFFI4162LKUA](/sequence-files/IGVFFI4162LKUA/), [IGVFFI6978FUZD](/sequence-files/IGVFFI6978FUZD/), [IGVFFI9775LKWN](/sequence-files/IGVFFI9775LKWN/), [IGVFFI6300DLLI](/sequence-files/IGVFFI6300DLLI/), [IGVFFI7042VJAP](/sequence-files/IGVFFI7042VJAP/) 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/IGVFDS7400NQET/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7400NQET](/measurement-sets/IGVFDS7400NQET/) has sequence file(s): [IGVFFI7288ZSLY](/sequence-files/IGVFFI7288ZSLY/), [IGVFFI5292DWTM](/sequence-files/IGVFFI5292DWTM/), [IGVFFI6153OKOT](/sequence-files/IGVFFI6153OKOT/), [IGVFFI4162LKUA](/sequence-files/IGVFFI4162LKUA/), [IGVFFI6978FUZD](/sequence-files/IGVFFI6978FUZD/), [IGVFFI9775LKWN](/sequence-files/IGVFFI9775LKWN/), [IGVFFI6300DLLI](/sequence-files/IGVFFI6300DLLI/), [IGVFFI7042VJAP](/sequence-files/IGVFFI7042VJAP/) 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/IGVFDS7400NQET/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing control for",
"detail": "Measurement set [IGVFDS7400NQET](/measurement-sets/IGVFDS7400NQET/) 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/IGVFDS7400NQET/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7400NQET](/measurement-sets/IGVFDS7400NQET/) 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/IGVFDS7400NQET/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS7400NQET](/measurement-sets/IGVFDS7400NQET/) 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/IGVFDS7400NQET/"
}
]
},
"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": "2023-11-30T22:46:02.088057+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/IGVFFI7288ZSLY/",
"accession": "IGVFFI7288ZSLY",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:27:06.452695+00:00",
"file_format": "fastq",
"file_size": 41565208,
"href": "/sequence-files/IGVFFI7288ZSLY/@@download/IGVFFI7288ZSLY.fastq.gz",
"md5sum": "756efa59c0eeade65867dedb67a73204",
"s3_uri": "s3://igvf-files/2023/12/05/5b48f50d-42d9-4e47-9b86-3901f954432a/IGVFFI7288ZSLY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-1-BinAll_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5292DWTM/",
"accession": "IGVFFI5292DWTM",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:01:43.811744+00:00",
"file_format": "fastq",
"file_size": 13929704,
"href": "/sequence-files/IGVFFI5292DWTM/@@download/IGVFFI5292DWTM.fastq.gz",
"md5sum": "ebeffcbfe866432dcc6ae8730a8679f4",
"s3_uri": "s3://igvf-files/2023/12/05/3bd44432-2212-425a-ac3d-7ac53d389531/IGVFFI5292DWTM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-1-BinAll_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6153OKOT/",
"accession": "IGVFFI6153OKOT",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:50:29.230118+00:00",
"file_format": "fastq",
"file_size": 14791415,
"href": "/sequence-files/IGVFFI6153OKOT/@@download/IGVFFI6153OKOT.fastq.gz",
"md5sum": "6978b8316a012520b3bc05de7c30ca2d",
"s3_uri": "s3://igvf-files/2023/12/05/ce8f44db-681c-42a4-bf4d-b85af9b7e38a/IGVFFI6153OKOT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-1-BinAll_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4162LKUA/",
"accession": "IGVFFI4162LKUA",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:56:02.322046+00:00",
"file_format": "fastq",
"file_size": 15290721,
"href": "/sequence-files/IGVFFI4162LKUA/@@download/IGVFFI4162LKUA.fastq.gz",
"md5sum": "719dc528de6a8a008f361b3e5ebd832c",
"s3_uri": "s3://igvf-files/2023/12/05/08f6af5c-cd01-4726-95f8-b4032de58fb0/IGVFFI4162LKUA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-2-BinAll_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6978FUZD/",
"accession": "IGVFFI6978FUZD",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:44:52.253413+00:00",
"file_format": "fastq",
"file_size": 78111572,
"href": "/sequence-files/IGVFFI6978FUZD/@@download/IGVFFI6978FUZD.fastq.gz",
"md5sum": "f599f3a47aee0ceff642f7ed2c5e011e",
"s3_uri": "s3://igvf-files/2023/12/05/cc80e503-b2d6-481d-af18-d8f6475657b3/IGVFFI6978FUZD.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-2-BinAll_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9775LKWN/",
"accession": "IGVFFI9775LKWN",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:32:50.536193+00:00",
"file_format": "fastq",
"file_size": 43181961,
"href": "/sequence-files/IGVFFI9775LKWN/@@download/IGVFFI9775LKWN.fastq.gz",
"md5sum": "da4d0ba45b04bce66e744fc40c5fbb2b",
"s3_uri": "s3://igvf-files/2023/12/05/d83c3d2a-51be-4f14-9a2c-6f1e89cc2f8e/IGVFFI9775LKWN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-2-BinAll_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6300DLLI/",
"accession": "IGVFFI6300DLLI",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:38:50.018335+00:00",
"file_format": "fastq",
"file_size": 74563408,
"href": "/sequence-files/IGVFFI6300DLLI/@@download/IGVFFI6300DLLI.fastq.gz",
"md5sum": "9d7b5b08c39a2c4165dd6173db4c3147",
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"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-1-BinAll_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7042VJAP/",
"accession": "IGVFFI7042VJAP",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:07:18.512359+00:00",
"file_format": "fastq",
"file_size": 14601901,
"href": "/sequence-files/IGVFFI7042VJAP/@@download/IGVFFI7042VJAP.fastq.gz",
"md5sum": "31cb74279d99b40f9fefaaba84ca6abd",
"s3_uri": "s3://igvf-files/2023/12/05/98fb7c4a-8ba4-4c99-ad37-1087c9ccdec9/IGVFFI7042VJAP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220228pPPIF-FFSample-4-D21-pPPIF-Amp-pPPIF-1-3-2-BinAll_I2_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": "2023-12-20T23:10:01.840363+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9690YXEE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9690YXEE",
"aliases": [
"jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-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": "2023-12-05T18:27:06.452695+00:00",
"summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "680517c0-0216-41f9-b684-390d78e80581"
}