{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6319CCJO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6319CCJO",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR1_Rep1_S137",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR1_Rep2_S192",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR2_Rep1_S143",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR2_Rep2_S198",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR3_Rep1_S149",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR3_Rep2_S204",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR4_Rep1_S155",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR4_Rep2_S210"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"ERROR": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6319CCJO](/measurement-sets/IGVFDS6319CCJO/) links to sample [IGVFSM8399ZECZ](/in-vitro-systems/IGVFSM8399ZECZ/) which links to auxiliary set [IGVFDS5394TNHK](/auxiliary-sets/IGVFDS5394TNHK/) but is not in its `auxiliary_sets`. Measurement sets are expected to link to auxiliary sets if they share the same sample.",
"level": 60,
"level_name": "ERROR",
"name": "audit_missing_auxiliary_set_link",
"path": "/measurement-sets/IGVFDS6319CCJO/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS6319CCJO](/measurement-sets/IGVFDS6319CCJO/) 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/IGVFDS6319CCJO/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6319CCJO](/measurement-sets/IGVFDS6319CCJO/) has sequence file(s) [IGVFFI4444YPRQ](/sequence-files/IGVFFI4444YPRQ/), [IGVFFI1162VBEH](/sequence-files/IGVFFI1162VBEH/), [IGVFFI1601HIKR](/sequence-files/IGVFFI1601HIKR/), [IGVFFI5750HKEP](/sequence-files/IGVFFI5750HKEP/), [IGVFFI1646OHQB](/sequence-files/IGVFFI1646OHQB/), [IGVFFI7037YPDM](/sequence-files/IGVFFI7037YPDM/), [IGVFFI1192EKYN](/sequence-files/IGVFFI1192EKYN/), [IGVFFI7956SVSZ](/sequence-files/IGVFFI7956SVSZ/) 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/IGVFDS6319CCJO/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6319CCJO](/measurement-sets/IGVFDS6319CCJO/) has revoked subobject auxiliary set [IGVFDS4580MCDT](/auxiliary-sets/IGVFDS4580MCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6319CCJO/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM8399ZECZ](/in-vitro-systems/IGVFSM8399ZECZ/) 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/IGVFSM8399ZECZ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing files",
"detail": "Auxiliary set [IGVFDS4580MCDT](/auxiliary-sets/IGVFDS4580MCDT/) has no `files`. File sets are expected to have files.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_no_files",
"path": "/auxiliary-sets/IGVFDS4580MCDT/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6319CCJO](/measurement-sets/IGVFDS6319CCJO/) 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/IGVFDS6319CCJO/"
},
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM8399ZECZ](/in-vitro-systems/IGVFSM8399ZECZ/) 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/IGVFSM8399ZECZ/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4580MCDT/",
"accession": "IGVFDS4580MCDT",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR1_Rep1_S137",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR1_Rep2_S192",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR2_Rep1_S143",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR2_Rep2_S198",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR3_Rep1_S149",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR3_Rep2_S204",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR4_Rep1_S155",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR4_Rep2_S210"
],
"file_set_type": "gRNA sequencing",
"status": "revoked"
}
],
"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/IGVFDS7857SYCK/",
"accession": "IGVFDS7857SYCK",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI3782KCTX/",
"accession": "IGVFFI3782KCTX",
"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": "2024-05-21T17:35:56.932404+00:00",
"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/IGVFFI1386YOTL/",
"accession": "IGVFFI1386YOTL",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR3_Rep1_S149"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:52:25.299127+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI1386YOTL/@@download/IGVFFI1386YOTL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/008d481a-6d58-4e4c-959a-3a2a94692a23/IGVFFI1386YOTL.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinC-PCR3_Rep1_S149.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI8805HMSN/",
"accession": "IGVFFI8805HMSN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR2_Rep1_S143"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:51:55.696000+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI8805HMSN/@@download/IGVFFI8805HMSN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/4e730c5c-f4eb-47e5-a61b-70eb3100fab9/IGVFFI8805HMSN.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinC-PCR2_Rep1_S143.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI0487EHSR/",
"accession": "IGVFFI0487EHSR",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR2_Rep2_S198"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:52:10.532626+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI0487EHSR/@@download/IGVFFI0487EHSR.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9a844a11-2f3c-4762-a39b-3e0a3ec9e235/IGVFFI0487EHSR.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinC-PCR2_Rep2_S198.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI4444YPRQ/",
"accession": "IGVFFI4444YPRQ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR1_Rep2_S192"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:06:40.867137+00:00",
"file_format": "fastq",
"file_size": 23856823,
"href": "/sequence-files/IGVFFI4444YPRQ/@@download/IGVFFI4444YPRQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/c3517f9b-2170-4b30-a53f-844eda4320ff/IGVFFI4444YPRQ.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/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinC-PCR1-Rep2_S192_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4069WDIB/",
"accession": "IGVFFI4069WDIB",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR1_Rep2_S192"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:51:40.635785+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI4069WDIB/@@download/IGVFFI4069WDIB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/7c9158b8-dc55-4cfd-b424-133e8a8a6e9e/IGVFFI4069WDIB.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinC-PCR1_Rep2_S192.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI6943QQTX/",
"accession": "IGVFFI6943QQTX",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR4_Rep2_S210"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:53:08.995911+00:00",
"file_format": "yaml",
"file_size": 913,
"href": "/configuration-files/IGVFFI6943QQTX/@@download/IGVFFI6943QQTX.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/283ca60e-cbdc-45f2-892a-eded7913e4e1/IGVFFI6943QQTX.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinC-PCR4_Rep2_S210.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI1162VBEH/",
"accession": "IGVFFI1162VBEH",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR3_Rep2_S204"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:07:56.889411+00:00",
"file_format": "fastq",
"file_size": 25586778,
"href": "/sequence-files/IGVFFI1162VBEH/@@download/IGVFFI1162VBEH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/3334a117-d2a7-4653-8853-80df8b877aed/IGVFFI1162VBEH.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/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinC-PCR3-Rep2_S204_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1601HIKR/",
"accession": "IGVFFI1601HIKR",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR4_Rep1_S155"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:08:15.371156+00:00",
"file_format": "fastq",
"file_size": 23682053,
"href": "/sequence-files/IGVFFI1601HIKR/@@download/IGVFFI1601HIKR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/419f4d58-a8aa-45d8-9cdf-97108f539835/IGVFFI1601HIKR.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/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinC-PCR4-Rep1_S155_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5827OXEA/",
"accession": "IGVFFI5827OXEA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR3_Rep2_S204"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:52:39.600974+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI5827OXEA/@@download/IGVFFI5827OXEA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/aac3ba7a-9e91-44d6-a5b7-91b689f85eba/IGVFFI5827OXEA.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinC-PCR3_Rep2_S204.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI3490BFEI/",
"accession": "IGVFFI3490BFEI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR4_Rep1_S155"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:52:54.167516+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI3490BFEI/@@download/IGVFFI3490BFEI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d93b3fb8-d768-491e-a923-0c45ef23702e/IGVFFI3490BFEI.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinC-PCR4_Rep1_S155.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/configuration-files/IGVFFI1237VLSC/",
"accession": "IGVFFI1237VLSC",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR1_Rep1_S137"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:51:25.885820+00:00",
"file_format": "yaml",
"file_size": 912,
"href": "/configuration-files/IGVFFI1237VLSC/@@download/IGVFFI1237VLSC.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/244c928a-48c0-49a8-86ce-34687ad71f7e/IGVFFI1237VLSC.yaml.gz",
"status": "released",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin6hrs-FF2-BinC-PCR1_Rep1_S137.yaml",
"upload_status": "validation exempted"
},
{
"@id": "/sequence-files/IGVFFI5750HKEP/",
"accession": "IGVFFI5750HKEP",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR2_Rep2_S198"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:07:19.289594+00:00",
"file_format": "fastq",
"file_size": 22084568,
"href": "/sequence-files/IGVFFI5750HKEP/@@download/IGVFFI5750HKEP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/674c7264-ac2f-434a-af77-054758b1c613/IGVFFI5750HKEP.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/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinC-PCR2-Rep2_S198_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1646OHQB/",
"accession": "IGVFFI1646OHQB",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR2_Rep1_S143"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:07:00.405004+00:00",
"file_format": "fastq",
"file_size": 24516207,
"href": "/sequence-files/IGVFFI1646OHQB/@@download/IGVFFI1646OHQB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/7fe89c82-3b2e-43d2-bfc4-bbe385cd393a/IGVFFI1646OHQB.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/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinC-PCR2-Rep1_S143_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7037YPDM/",
"accession": "IGVFFI7037YPDM",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR3_Rep1_S149"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:07:37.887444+00:00",
"file_format": "fastq",
"file_size": 18576245,
"href": "/sequence-files/IGVFFI7037YPDM/@@download/IGVFFI7037YPDM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/70b574c0-1ac0-431a-ae8b-744be0169218/IGVFFI7037YPDM.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/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinC-PCR3-Rep1_S149_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1192EKYN/",
"accession": "IGVFFI1192EKYN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR4_Rep2_S210"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:08:34.196998+00:00",
"file_format": "fastq",
"file_size": 23403608,
"href": "/sequence-files/IGVFFI1192EKYN/@@download/IGVFFI1192EKYN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/156b9864-4099-417f-986b-b363ce331c62/IGVFFI1192EKYN.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/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinC-PCR4-Rep2_S210_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7956SVSZ/",
"accession": "IGVFFI7956SVSZ",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR1_Rep1_S137"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-06-01T02:06:18.689810+00:00",
"file_format": "fastq",
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"s3_uri": "s3://igvf-files/2024/06/01/8a559285-b42e-4537-9098-a3e3e71f93cc/IGVFFI7956SVSZ.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/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinC-PCR1-Rep1_S137_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4544YEQM/"
],
"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": "2024-07-10T19:48:40.612653+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8399ZECZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8399ZECZ",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR1_Rep1_S137",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR1_Rep2_S192",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR2_Rep1_S143",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR2_Rep2_S198",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR3_Rep1_S149",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR3_Rep2_S204",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR4_Rep1_S155",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin6hrs-FF2-BinC-PCR4_Rep2_S210"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"modality": "degradation",
"status": "released"
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"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 C for 35-45% expression of MYC) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"purpose": "activation",
"status": "released",
"summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T02:06:18.689810+00:00",
"summary": "mixed CRISPR FlowFISH screen sorted on the expression of MYC integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"targeted_genes": [
{
"@id": "/genes/ENSG00000136997/",
"geneid": "ENSG00000136997",
"name": "MYC proto-oncogene, bHLH transcription factor",
"status": "released",
"symbol": "MYC",
"synonyms": [
"bHLHe39",
"myc-related translation/localization regulatory factor",
"MYC proto-oncogene, bHLH transcription factor",
"MYC",
"c-Myc",
"v-myc avian myelocytomatosis viral oncogene homolog",
"proto-oncogene c-Myc",
"transcription factor p64",
"myc proto-oncogene protein",
"avian myelocytomatosis viral oncogene homolog",
"MRTL",
"class E basic helix-loop-helix protein 39",
"MYCC",
"v-myc myelocytomatosis viral oncogene homolog"
]
}
],
"uuid": "608d2c94-21a0-48ca-9033-9d957b7f6ffb"
}