{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9168ZKDC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9168ZKDC",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR1_S1",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR2_S7",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR3_S97",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR4_S103"
],
"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": "missing publication",
"detail": "In vitro system [IGVFSM8111MLZW](/in-vitro-systems/IGVFSM8111MLZW/) 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/IGVFSM8111MLZW/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9168ZKDC](/measurement-sets/IGVFDS9168ZKDC/) 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/IGVFDS9168ZKDC/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9168ZKDC](/measurement-sets/IGVFDS9168ZKDC/) has sequence file(s) [IGVFFI9605MXIW](/sequence-files/IGVFFI9605MXIW/), [IGVFFI9053ATLK](/sequence-files/IGVFFI9053ATLK/), [IGVFFI3274GRZY](/sequence-files/IGVFFI3274GRZY/), [IGVFFI2171OGJO](/sequence-files/IGVFFI2171OGJO/) 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/IGVFDS9168ZKDC/"
},
{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS9621FJCZ](/auxiliary-sets/IGVFDS9621FJCZ/) 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": "/auxiliary-sets/IGVFDS9621FJCZ/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM8111MLZW](/in-vitro-systems/IGVFSM8111MLZW/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM8111MLZW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9621FJCZ/",
"accession": "IGVFDS9621FJCZ",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_KITLG-Auxin0hrs-FF1"
],
"file_set_type": "cell sorting",
"status": "released"
}
],
"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/IGVFDS7846UISG/",
"accession": "IGVFDS7846UISG",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI5995VHKI/",
"accession": "IGVFFI5995VHKI",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2024-05-16T17:32:26.522591+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"documents": [
"/documents/74d53b9c-ab1d-42e3-b679-d3a00ae3d842/"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI9605MXIW/",
"accession": "IGVFFI9605MXIW",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR3_S97"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:10:52.072437+00:00",
"file_format": "fastq",
"file_size": 36290095,
"href": "/sequence-files/IGVFFI9605MXIW/@@download/IGVFFI9605MXIW.fastq.gz",
"md5sum": "c3b9923da7b1b80701c5fa2e7b3cf3b5",
"s3_uri": "s3://igvf-files/2024/06/01/03ddcdcd-6ff3-4326-953b-d55ac9f7d0dc/IGVFFI9605MXIW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinA-PCR3_S97_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8677QAFW/",
"accession": "IGVFFI8677QAFW",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR3_S97"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:08.193076+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI8677QAFW/@@download/IGVFFI8677QAFW.yaml.gz",
"md5sum": "591ae89a19b3aa6673345e4940e5c016",
"s3_uri": "s3://igvf-files/2024/06/11/f559802a-e29a-4055-8dd7-57e4bd29b6ed/IGVFFI8677QAFW.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinA-PCR3_S97.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI4323OUFB/",
"accession": "IGVFFI4323OUFB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR4_S103"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:21.523457+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI4323OUFB/@@download/IGVFFI4323OUFB.yaml.gz",
"md5sum": "30637021b1b226525e1efe7ea3c55704",
"s3_uri": "s3://igvf-files/2024/06/11/bdf95efb-ed69-4006-979c-4866ade46c1f/IGVFFI4323OUFB.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinA-PCR4_S103.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI8363ADQK/",
"accession": "IGVFFI8363ADQK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR2_S7"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:05:54.683371+00:00",
"file_format": "yaml",
"file_size": 900,
"href": "/configuration-files/IGVFFI8363ADQK/@@download/IGVFFI8363ADQK.yaml.gz",
"md5sum": "58c7dc9c4bfb353cb5efb2786525f679",
"s3_uri": "s3://igvf-files/2024/06/11/0ea6d0f8-a3c1-40c2-b6c2-10325701ac3f/IGVFFI8363ADQK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinA-PCR2_S7.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI9053ATLK/",
"accession": "IGVFFI9053ATLK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR1_S1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:10:11.339608+00:00",
"file_format": "fastq",
"file_size": 10662322,
"href": "/sequence-files/IGVFFI9053ATLK/@@download/IGVFFI9053ATLK.fastq.gz",
"md5sum": "a6f391dbf9fc3e631424da5a86e5f48e",
"s3_uri": "s3://igvf-files/2024/06/01/2ffb14a1-4976-4f07-9d8b-2b1ac7da8848/IGVFFI9053ATLK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008565/",
"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinA-PCR1_S1_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8642JEKZ/",
"accession": "IGVFFI8642JEKZ",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR1_S1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:05:27.129924+00:00",
"file_format": "yaml",
"file_size": 900,
"href": "/configuration-files/IGVFFI8642JEKZ/@@download/IGVFFI8642JEKZ.yaml.gz",
"md5sum": "5be6e515144186c24332516ab5dfa463",
"s3_uri": "s3://igvf-files/2024/06/11/b49bc8c0-8ece-45ad-866c-a87b53780364/IGVFFI8642JEKZ.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinA-PCR1_S1.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI3274GRZY/",
"accession": "IGVFFI3274GRZY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR4_S103"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:11:10.226683+00:00",
"file_format": "fastq",
"file_size": 20053603,
"href": "/sequence-files/IGVFFI3274GRZY/@@download/IGVFFI3274GRZY.fastq.gz",
"md5sum": "8125a17dbd2ef39f5202f97b24092788",
"s3_uri": "s3://igvf-files/2024/06/01/90ae2cb4-44ec-473d-8e7f-d041642ab65c/IGVFFI3274GRZY.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinA-PCR4_S103_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2171OGJO/",
"accession": "IGVFFI2171OGJO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR2_S7"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:10:30.356025+00:00",
"file_format": "fastq",
"file_size": 8424943,
"href": "/sequence-files/IGVFFI2171OGJO/@@download/IGVFFI2171OGJO.fastq.gz",
"md5sum": "204549bdcc894dd20aba02803efa2770",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina HiSeq 2500"
},
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220104B013_Cohesin_KITLG/fastq_trim/Auxin0hrs-FF1-BinA-PCR2_S7_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6482AXWW/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "CRISPR FlowFISH screen",
"protocols": [
"https://www.protocols.io/view/crispri-of-regulatory-elements-upon-degron-operati-5jyl82d59l2w/v1"
],
"release_timestamp": "2024-07-10T19:41:52.663779+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8111MLZW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8111MLZW",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR1_S1",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR2_S7",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR3_S97",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinA-PCR4_S103"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "Homo sapiens (male) HCT116 cell line (sorting details: FACS bin A for 0-10% expression of KITLG) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T02:10:11.339608+00:00",
"summary": "mixed CRISPR FlowFISH screen sorted on the expression of KITLG integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"targeted_genes": [
{
"@id": "/genes/ENSG00000049130/",
"geneid": "ENSG00000049130",
"name": "KIT ligand",
"status": "released",
"symbol": "KITLG",
"synonyms": [
"SF",
"WS2F",
"Kitl",
"FPH2",
"SCF",
"KL-1",
"DFNA69",
"familial progressive hyperpigmentation 2",
"mast cell growth factor",
"DCUA",
"kit ligand",
"c-Kit ligand",
"SLF",
"steel factor",
"KITLG",
"SHEP7",
"stem cell factor",
"KIT ligand",
"FPHH",
"MGF"
]
}
],
"uuid": "a0077c5a-dc49-47d4-9fea-0894fcaa4b9f"
}