{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS9738NANI/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS9738NANI",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep1_S25",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep2_S80",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep1_S31",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep2_S86",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep1_S37",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep2_S92",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep1_S43",
"jesse-engreitz:auxiliary_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep2_S98"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO0384OZRW](/human-donors/IGVFDO0384OZRW/) has in progress subobject publication [155f24ce-5c2c-4400-8651-da9447eaca25](/publications/155f24ce-5c2c-4400-8651-da9447eaca25/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO0384OZRW/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9738NANI](/auxiliary-sets/IGVFDS9738NANI/) has sequence file(s) [IGVFFI0450VGJL](/sequence-files/IGVFFI0450VGJL/), [IGVFFI4364CKDK](/sequence-files/IGVFFI4364CKDK/), [IGVFFI6307WYZS](/sequence-files/IGVFFI6307WYZS/), [IGVFFI0700SJDG](/sequence-files/IGVFFI0700SJDG/), [IGVFFI0269PZHU](/sequence-files/IGVFFI0269PZHU/), [IGVFFI2787YXFO](/sequence-files/IGVFFI2787YXFO/), [IGVFFI3163PWLN](/sequence-files/IGVFFI3163PWLN/), [IGVFFI3236SBJX](/sequence-files/IGVFFI3236SBJX/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS9738NANI/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS9738NANI](/auxiliary-sets/IGVFDS9738NANI/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS9738NANI/"
}
]
},
"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"
},
"control_for": [],
"creation_timestamp": "2024-05-21T17:13:05.953865+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
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{
"@id": "/sequence-files/IGVFFI0450VGJL/",
"accession": "IGVFFI0450VGJL",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep1_S25"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:00:44.627135+00:00",
"file_format": "fastq",
"file_size": 40004540,
"href": "/sequence-files/IGVFFI0450VGJL/@@download/IGVFFI0450VGJL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/a3e5f1ab-0af5-4306-8272-b2484431a776/IGVFFI0450VGJL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8320WTKY/",
"accession": "IGVFFI8320WTKY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep1_S25"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:25.114540+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI8320WTKY/@@download/IGVFFI8320WTKY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/460c8fc2-6b65-4898-84fe-94b229fa9b97/IGVFFI8320WTKY.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinA-PCR1_Rep1_S25.yaml",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4364CKDK/",
"accession": "IGVFFI4364CKDK",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep2_S80"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:01:05.758040+00:00",
"file_format": "fastq",
"file_size": 17865577,
"href": "/sequence-files/IGVFFI4364CKDK/@@download/IGVFFI4364CKDK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/ad0d7cdc-3d4b-4e1e-a82e-794013b26cd2/IGVFFI4364CKDK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinA-PCR1-Rep2_S80_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6307WYZS/",
"accession": "IGVFFI6307WYZS",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep1_S31"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:01:25.917425+00:00",
"file_format": "fastq",
"file_size": 47247911,
"href": "/sequence-files/IGVFFI6307WYZS/@@download/IGVFFI6307WYZS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/5daa8159-99a1-41d5-a28b-e92120fec35c/IGVFFI6307WYZS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinA-PCR2-Rep1_S31_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0700SJDG/",
"accession": "IGVFFI0700SJDG",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep1_S43"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:02:52.921577+00:00",
"file_format": "fastq",
"file_size": 34358898,
"href": "/sequence-files/IGVFFI0700SJDG/@@download/IGVFFI0700SJDG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/aab548e2-6b82-4e91-a6d5-c750ebd8a571/IGVFFI0700SJDG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinA-PCR4-Rep1_S43_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0269PZHU/",
"accession": "IGVFFI0269PZHU",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep1_S37"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:02:11.613420+00:00",
"file_format": "fastq",
"file_size": 41754604,
"href": "/sequence-files/IGVFFI0269PZHU/@@download/IGVFFI0269PZHU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/c620f2c2-a807-4315-b41f-071c9149963b/IGVFFI0269PZHU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinA-PCR3-Rep1_S37_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2787YXFO/",
"accession": "IGVFFI2787YXFO",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep2_S86"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:01:50.554640+00:00",
"file_format": "fastq",
"file_size": 39154776,
"href": "/sequence-files/IGVFFI2787YXFO/@@download/IGVFFI2787YXFO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/e636c19b-b31f-4810-bc89-9774df55f5f1/IGVFFI2787YXFO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinA-PCR2-Rep2_S86_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3163PWLN/",
"accession": "IGVFFI3163PWLN",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep2_S98"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:03:13.807261+00:00",
"file_format": "fastq",
"file_size": 26291268,
"href": "/sequence-files/IGVFFI3163PWLN/@@download/IGVFFI3163PWLN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/fea235a9-8a0a-44d5-91df-2715f180519b/IGVFFI3163PWLN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinA-PCR4-Rep2_S98_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3236SBJX/",
"accession": "IGVFFI3236SBJX",
"aliases": [
"jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep2_S92"
],
"content_type": "reads",
"creation_timestamp": "2024-06-01T02:02:32.272242+00:00",
"file_format": "fastq",
"file_size": 17391101,
"href": "/sequence-files/IGVFFI3236SBJX/@@download/IGVFFI3236SBJX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/01/de0f31fd-ab7f-4a80-81eb-fb12d2fa758a/IGVFFI3236SBJX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008565/",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinA-PCR3-Rep2_S92_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9283MPSI/",
"accession": "IGVFFI9283MPSI",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep2_S86"
],
"content_type": "seqspec",
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"file_format": "yaml",
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"href": "/configuration-files/IGVFFI9283MPSI/@@download/IGVFFI9283MPSI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/9cef3a7f-1d2c-4d3b-a0d6-59756f63c8ab/IGVFFI9283MPSI.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinA-PCR2_Rep2_S86.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1697OBKN/",
"accession": "IGVFFI1697OBKN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep1_S37"
],
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"file_size": 911,
"href": "/configuration-files/IGVFFI1697OBKN/@@download/IGVFFI1697OBKN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/a762de24-a8c9-44c3-a616-39d0fb840a54/IGVFFI1697OBKN.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinA-PCR3_Rep1_S37.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6808FPSN/",
"accession": "IGVFFI6808FPSN",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep1_S31"
],
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"creation_timestamp": "2024-06-11T20:47:54.180610+00:00",
"file_format": "yaml",
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"href": "/configuration-files/IGVFFI6808FPSN/@@download/IGVFFI6808FPSN.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/0da87408-111a-4209-b58d-4bc9805d8556/IGVFFI6808FPSN.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinA-PCR2_Rep1_S31.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1710IDES/",
"accession": "IGVFFI1710IDES",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep1_S43"
],
"content_type": "seqspec",
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"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI1710IDES/@@download/IGVFFI1710IDES.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/d6ceceaf-7ec4-4412-8b7d-9c0dbb0a7dce/IGVFFI1710IDES.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinA-PCR4_Rep1_S43.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4380QFIT/",
"accession": "IGVFFI4380QFIT",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep2_S80"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:47:39.745979+00:00",
"file_format": "yaml",
"file_size": 911,
"href": "/configuration-files/IGVFFI4380QFIT/@@download/IGVFFI4380QFIT.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/8e858a1e-6440-41e3-91b1-4ef0f8e6aa3a/IGVFFI4380QFIT.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinA-PCR1_Rep2_S80.yaml",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3170BIJY/",
"accession": "IGVFFI3170BIJY",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep2_S92"
],
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"href": "/configuration-files/IGVFFI3170BIJY/@@download/IGVFFI3170BIJY.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/197ab0dc-d542-4e06-ab3b-ce9985d9f008/IGVFFI3170BIJY.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7979CDQA/",
"accession": "IGVFFI7979CDQA",
"aliases": [
"jesse-engreitz:seqspecfile_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep2_S98"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-11T20:49:06.175220+00:00",
"file_format": "yaml",
"file_size": 910,
"href": "/configuration-files/IGVFFI7979CDQA/@@download/IGVFFI7979CDQA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/11/5cb64e80-f084-45fd-a858-9c1d2a3e4fe2/IGVFFI7979CDQA.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.MYC-Auxin0hrs-FF2-BinA-PCR4_Rep2_S98.yaml",
"upload_status": "validated"
}
],
"input_file_set_for": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS3856ZADL/",
"accession": "IGVFDS3856ZADL",
"aliases": [
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep1_S25",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep2_S80",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep1_S31",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep2_S86",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep1_S37",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep2_S92",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep1_S43",
"jesse-engreitz:measurement_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep2_S98"
],
"preferred_assay_title": "CRISPR FlowFISH screen"
}
],
"release_timestamp": "2024-07-10T20:19:57.891711+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6871QVFB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6871QVFB",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep1_S25",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR1_Rep2_S80",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep1_S31",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR2_Rep2_S86",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep1_S37",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR3_Rep2_S92",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep1_S43",
"jesse-engreitz:in-vitro-system_CRUDO_MYC-Auxin0hrs-FF2-BinA-PCR4_Rep2_S98"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7857SYCK/"
],
"modifications": [
"/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin A for 0-10% expression of MYC) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T02:00:44.627135+00:00",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "ea37e9fc-cb66-4736-9b8c-d94f39ff6795"
}