{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7789CCCR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7789CCCR",
"aliases": [
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR1_S6",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR2_S12",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR3_S102",
"jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR4_S108"
],
"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": "Measurement set [IGVFDS7789CCCR](/measurement-sets/IGVFDS7789CCCR/) 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/IGVFDS7789CCCR/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7789CCCR](/measurement-sets/IGVFDS7789CCCR/) has sequence file(s) [IGVFFI3880FPSK](/sequence-files/IGVFFI3880FPSK/), [IGVFFI1910QCOP](/sequence-files/IGVFFI1910QCOP/), [IGVFFI6575LYZN](/sequence-files/IGVFFI6575LYZN/), [IGVFFI7770QKUY](/sequence-files/IGVFFI7770QKUY/) 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/IGVFDS7789CCCR/"
},
{
"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/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM9117BTSA](/in-vitro-systems/IGVFSM9117BTSA/) 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/IGVFSM9117BTSA/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM9117BTSA](/in-vitro-systems/IGVFSM9117BTSA/) 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/IGVFSM9117BTSA/"
}
]
},
"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": "2024-05-16T17:32:34.733361+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": "/configuration-files/IGVFFI7676KGCV/",
"accession": "IGVFFI7676KGCV",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR4_S108"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:32.856796+00:00",
"file_format": "yaml",
"file_size": 904,
"href": "/configuration-files/IGVFFI7676KGCV/@@download/IGVFFI7676KGCV.yaml.gz",
"md5sum": "5b8904f515831b1e246072a217566d1f",
"s3_uri": "s3://igvf-files/2024/06/11/5e09aac3-5770-4ca0-bcc4-ed52f679cb30/IGVFFI7676KGCV.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinF-PCR4_S108.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI3880FPSK/",
"accession": "IGVFFI3880FPSK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR2_S12"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:10:49.254748+00:00",
"file_format": "fastq",
"file_size": 15427391,
"href": "/sequence-files/IGVFFI3880FPSK/@@download/IGVFFI3880FPSK.fastq.gz",
"md5sum": "dc9e8a19501dfb16ddf2692627db1027",
"s3_uri": "s3://igvf-files/2024/06/01/a8376b5f-7bb3-439a-b441-8ab5607abb3d/IGVFFI3880FPSK.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-BinF-PCR2_S12_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0059WNTR/",
"accession": "IGVFFI0059WNTR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR3_S102"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:19.359333+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI0059WNTR/@@download/IGVFFI0059WNTR.yaml.gz",
"md5sum": "23aebf28dfca0986004e9d24f4a8b4c4",
"s3_uri": "s3://igvf-files/2024/06/11/2b61137f-8665-44a6-abec-7caeba4b818d/IGVFFI0059WNTR.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinF-PCR3_S102.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI8582UZLK/",
"accession": "IGVFFI8582UZLK",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR1_S6"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:05:52.442076+00:00",
"file_format": "yaml",
"file_size": 902,
"href": "/configuration-files/IGVFFI8582UZLK/@@download/IGVFFI8582UZLK.yaml.gz",
"md5sum": "1c4f2d460886d8f01e3ffc983f549bf5",
"s3_uri": "s3://igvf-files/2024/06/11/6c4670fd-06f5-4a7f-910d-54b4d2073030/IGVFFI8582UZLK.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinF-PCR1_S6.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1199IUIN/",
"accession": "IGVFFI1199IUIN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR2_S12"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T22:06:05.952559+00:00",
"file_format": "yaml",
"file_size": 901,
"href": "/configuration-files/IGVFFI1199IUIN/@@download/IGVFFI1199IUIN.yaml.gz",
"md5sum": "a2668176490b0252bc9ce817fb17bff6",
"s3_uri": "s3://igvf-files/2024/06/11/29d519de-2697-4f9f-92c6-a47dce07add3/IGVFFI1199IUIN.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.Auxin0hrs-FF1-BinF-PCR2_S12.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI1910QCOP/",
"accession": "IGVFFI1910QCOP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR3_S102"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:11:07.268875+00:00",
"file_format": "fastq",
"file_size": 38522468,
"href": "/sequence-files/IGVFFI1910QCOP/@@download/IGVFFI1910QCOP.fastq.gz",
"md5sum": "e322207e9a8b23047cf933473423f15e",
"s3_uri": "s3://igvf-files/2024/06/01/48867b74-44ca-4b5f-9fa7-9f99164aa891/IGVFFI1910QCOP.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-BinF-PCR3_S102_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6575LYZN/",
"accession": "IGVFFI6575LYZN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR1_S6"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:10:27.221651+00:00",
"file_format": "fastq",
"file_size": 20442777,
"href": "/sequence-files/IGVFFI6575LYZN/@@download/IGVFFI6575LYZN.fastq.gz",
"md5sum": "e8197300aaac8874c383f26d53a9b35b",
"s3_uri": "s3://igvf-files/2024/06/01/b4defe1a-4c01-4616-8e48-91b24f734f41/IGVFFI6575LYZN.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-BinF-PCR1_S6_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7770QKUY/",
"accession": "IGVFFI7770QKUY",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR4_S108"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:14:26.364740+00:00",
"file_format": "fastq",
"file_size": 44307926,
"href": "/sequence-files/IGVFFI7770QKUY/@@download/IGVFFI7770QKUY.fastq.gz",
"md5sum": "2c19d2a6482886c96b160bc66b66b449",
"s3_uri": "s3://igvf-files/2024/06/01/8bcdf0c8-2be2-446e-9da5-86b984d2db15/IGVFFI7770QKUY.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-BinF-PCR4_S108_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": "2024-07-10T19:42:21.527306+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9117BTSA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9117BTSA",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR1_S6",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR2_S12",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR3_S102",
"jesse-engreitz:in-vitro-system_CRUDO_KITLG-Auxin0hrs-FF1-BinF-PCR4_S108"
],
"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 F for 80-100% 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": "2024-06-01T02:10:27.221651+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": "bdbc242f-95af-403e-87fc-45e05be8d89d"
}