{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7135ULJC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7135ULJC",
"aliases": [
"jesse-engreitz:measurement_CRUDO_TAPseq-Auxin0hrs-Rep2"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003660/",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"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 [IGVFDS8748OHPQ](/auxiliary-sets/IGVFDS8748OHPQ/) has sequence file(s) [IGVFFI2315CHAW](/sequence-files/IGVFFI2315CHAW/), [IGVFFI6591FOMG](/sequence-files/IGVFFI6591FOMG/), [IGVFFI1413KOZF](/sequence-files/IGVFFI1413KOZF/), [IGVFFI2373VGQQ](/sequence-files/IGVFFI2373VGQQ/), [IGVFFI5632DOTG](/sequence-files/IGVFFI5632DOTG/), [IGVFFI0448FLMO](/sequence-files/IGVFFI0448FLMO/), [IGVFFI5285IRWT](/sequence-files/IGVFFI5285IRWT/), [IGVFFI8825PYZU](/sequence-files/IGVFFI8825PYZU/), [IGVFFI6297ZONU](/sequence-files/IGVFFI6297ZONU/), [IGVFFI6523ECXR](/sequence-files/IGVFFI6523ECXR/), [IGVFFI7983EOQT](/sequence-files/IGVFFI7983EOQT/), [IGVFFI1717NNGG](/sequence-files/IGVFFI1717NNGG/) 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/IGVFDS8748OHPQ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7135ULJC](/measurement-sets/IGVFDS7135ULJC/) has sequence file(s) [IGVFFI7624ITNU](/sequence-files/IGVFFI7624ITNU/), [IGVFFI1923YHHK](/sequence-files/IGVFFI1923YHHK/), [IGVFFI8450TDKJ](/sequence-files/IGVFFI8450TDKJ/), [IGVFFI4471BAWM](/sequence-files/IGVFFI4471BAWM/), [IGVFFI7281TZZG](/sequence-files/IGVFFI7281TZZG/), [IGVFFI2893MYCT](/sequence-files/IGVFFI2893MYCT/), [IGVFFI4178KSHJ](/sequence-files/IGVFFI4178KSHJ/), [IGVFFI8305FKDJ](/sequence-files/IGVFFI8305FKDJ/), [IGVFFI5311ZUSI](/sequence-files/IGVFFI5311ZUSI/), [IGVFFI6429AOLS](/sequence-files/IGVFFI6429AOLS/), [IGVFFI7941GPIL](/sequence-files/IGVFFI7941GPIL/), [IGVFFI2780VBGU](/sequence-files/IGVFFI2780VBGU/) 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": "/measurement-sets/IGVFDS7135ULJC/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8748OHPQ/",
"accession": "IGVFDS8748OHPQ",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_TAPseq-Auxin0hrs-Rep2"
],
"file_set_type": "gRNA sequencing"
}
],
"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": "2024-05-23T22:48:13.532781+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"
}
],
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7624ITNU/",
"accession": "IGVFFI7624ITNU",
"aliases": [
"jesse-engreitz:measurement_files_CRUDO_TAPseq-Auxin0hrs-Rep2_S2_I1"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:12:08.961174+00:00",
"file_format": "fastq",
"file_size": 116046906,
"href": "/sequence-files/IGVFFI7624ITNU/@@download/IGVFFI7624ITNU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/51b4b2ee-395a-4e61-9189-ce0db3d17340/IGVFFI7624ITNU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L378_S1_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1923YHHK/",
"accession": "IGVFFI1923YHHK",
"aliases": [
"jesse-engreitz:measurement_files_CRUDO_TAPseq-Auxin0hrs-Rep2_S3_R1"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:12:12.785227+00:00",
"file_format": "fastq",
"file_size": 398954551,
"href": "/sequence-files/IGVFFI1923YHHK/@@download/IGVFFI1923YHHK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/1d1b8c75-aca0-451b-a265-009ba161b1d5/IGVFFI1923YHHK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L378_S1_L003_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8450TDKJ/",
"accession": "IGVFFI8450TDKJ",
"aliases": [
"jesse-engreitz:measurement_files_CRUDO_TAPseq-Auxin0hrs-Rep2_S3_I1"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:12:24.688913+00:00",
"file_format": "fastq",
"file_size": 116628550,
"href": "/sequence-files/IGVFFI8450TDKJ/@@download/IGVFFI8450TDKJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/c41fe3a7-b204-459a-b617-f214d6458996/IGVFFI8450TDKJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L378_S1_L003_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4471BAWM/",
"accession": "IGVFFI4471BAWM",
"aliases": [
"jesse-engreitz:measurement_files_CRUDO_TAPseq-Auxin0hrs-Rep2_S4_R1"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:12:28.487514+00:00",
"file_format": "fastq",
"file_size": 396518650,
"href": "/sequence-files/IGVFFI4471BAWM/@@download/IGVFFI4471BAWM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/3402daac-e083-458a-a78b-308e80f911dd/IGVFFI4471BAWM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L378_S1_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7281TZZG/",
"accession": "IGVFFI7281TZZG",
"aliases": [
"jesse-engreitz:measurement_files_CRUDO_TAPseq-Auxin0hrs-Rep2_S4_R2"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:12:33.144928+00:00",
"file_format": "fastq",
"file_size": 890324466,
"href": "/sequence-files/IGVFFI7281TZZG/@@download/IGVFFI7281TZZG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/cb0f3b8e-f6c6-44fc-ab1f-7732919fd9ac/IGVFFI7281TZZG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L378_S1_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2893MYCT/",
"accession": "IGVFFI2893MYCT",
"aliases": [
"jesse-engreitz:measurement_files_CRUDO_TAPseq-Auxin0hrs-Rep2_S2_R1"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:11:53.989163+00:00",
"file_format": "fastq",
"file_size": 389722421,
"href": "/sequence-files/IGVFFI2893MYCT/@@download/IGVFFI2893MYCT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/5d609905-849c-4977-8d09-a4680c87554e/IGVFFI2893MYCT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L378_S1_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4178KSHJ/",
"accession": "IGVFFI4178KSHJ",
"aliases": [
"jesse-engreitz:measurement_files_CRUDO_TAPseq-Auxin0hrs-Rep2_S2_R2"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:11:58.686924+00:00",
"file_format": "fastq",
"file_size": 875077203,
"href": "/sequence-files/IGVFFI4178KSHJ/@@download/IGVFFI4178KSHJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/140e84ff-9a70-4cd1-80c5-9cb87e59006d/IGVFFI4178KSHJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L378_S1_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8305FKDJ/",
"accession": "IGVFFI8305FKDJ",
"aliases": [
"jesse-engreitz:measurement_files_CRUDO_TAPseq-Auxin0hrs-Rep2_S4_I1"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:12:40.615288+00:00",
"file_format": "fastq",
"file_size": 117297474,
"href": "/sequence-files/IGVFFI8305FKDJ/@@download/IGVFFI8305FKDJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/735464da-916a-451e-b892-d3b087fe1c7e/IGVFFI8305FKDJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L378_S1_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5311ZUSI/",
"accession": "IGVFFI5311ZUSI",
"aliases": [
"jesse-engreitz:measurement_files_CRUDO_TAPseq-Auxin0hrs-Rep2_S1_R2"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:11:43.461114+00:00",
"file_format": "fastq",
"file_size": 882680443,
"href": "/sequence-files/IGVFFI5311ZUSI/@@download/IGVFFI5311ZUSI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/808cd2ed-9624-42ab-895d-dab4f4ddfa26/IGVFFI5311ZUSI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L378_S1_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6429AOLS/",
"accession": "IGVFFI6429AOLS",
"aliases": [
"jesse-engreitz:measurement_files_CRUDO_TAPseq-Auxin0hrs-Rep2_S1_R1"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:11:36.315221+00:00",
"file_format": "fastq",
"file_size": 391643311,
"href": "/sequence-files/IGVFFI6429AOLS/@@download/IGVFFI6429AOLS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/655d6ce8-4b1f-40ce-b542-d27822498095/IGVFFI6429AOLS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L378_S1_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7941GPIL/",
"accession": "IGVFFI7941GPIL",
"aliases": [
"jesse-engreitz:measurement_files_CRUDO_TAPseq-Auxin0hrs-Rep2_S1_I1"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:11:50.302691+00:00",
"file_format": "fastq",
"file_size": 115749125,
"href": "/sequence-files/IGVFFI7941GPIL/@@download/IGVFFI7941GPIL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/977efc38-f417-4993-b495-98bfe5eb867e/IGVFFI7941GPIL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L378_S1_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2780VBGU/",
"accession": "IGVFFI2780VBGU",
"aliases": [
"jesse-engreitz:measurement_files_CRUDO_TAPseq-Auxin0hrs-Rep2_S3_R2"
],
"content_type": "reads",
"creation_timestamp": "2024-06-03T19:12:17.706188+00:00",
"file_format": "fastq",
"file_size": 898031316,
"href": "/sequence-files/IGVFFI2780VBGU/@@download/IGVFFI2780VBGU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/06/03/44077e24-4ce7-49a3-9d7f-08499d831a04/IGVFFI2780VBGU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"term_name": "Illumina NextSeq 550"
},
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/221224_Cohesin_TAPseq_v2/221219_P044_cohesin_tapseq_v2/outs/fastq_path/L378_S1_L003_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9196QXOM/",
"accession": "IGVFFI9196QXOM",
"aliases": [
"jesse-engreitz:seqspecfile_rna_CRUDO_TAPseq_Auxin0hrs-Rep2-S1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-20T17:15:57.026263+00:00",
"file_format": "yaml",
"file_size": 1046,
"href": "/configuration-files/IGVFFI9196QXOM/@@download/IGVFFI9196QXOM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/20/5a5d7204-169a-472a-b2d9-670d6c70d0e5/IGVFFI9196QXOM.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/tapseq_seqspec.out.Auxin0hrs-Rep2-S1.rna.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7257YBUF/",
"accession": "IGVFFI7257YBUF",
"aliases": [
"jesse-engreitz:seqspecfile_rna_CRUDO_TAPseq_Auxin0hrs-Rep2-S2"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-20T17:16:02.452257+00:00",
"file_format": "yaml",
"file_size": 1045,
"href": "/configuration-files/IGVFFI7257YBUF/@@download/IGVFFI7257YBUF.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/20/23bc1a24-2e1d-45bd-bc66-c2d76fe52a9c/IGVFFI7257YBUF.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/tapseq_seqspec.out.Auxin0hrs-Rep2-S2.rna.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5208SSVS/",
"accession": "IGVFFI5208SSVS",
"aliases": [
"jesse-engreitz:seqspecfile_rna_CRUDO_TAPseq_Auxin0hrs-Rep2-S3"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-20T17:16:07.594701+00:00",
"file_format": "yaml",
"file_size": 1046,
"href": "/configuration-files/IGVFFI5208SSVS/@@download/IGVFFI5208SSVS.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/20/1a1b16f5-9049-4eda-8320-40bfbcdb6c14/IGVFFI5208SSVS.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/tapseq_seqspec.out.Auxin0hrs-Rep2-S3.rna.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9662WYOI/",
"accession": "IGVFFI9662WYOI",
"aliases": [
"jesse-engreitz:seqspecfile_rna_CRUDO_TAPseq_Auxin0hrs-Rep2-S4"
],
"content_type": "seqspec",
"creation_timestamp": "2024-06-20T17:16:12.694452+00:00",
"file_format": "yaml",
"file_size": 1044,
"href": "/configuration-files/IGVFFI9662WYOI/@@download/IGVFFI9662WYOI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/06/20/91edda77-6fbd-4118-9d97-0440e826e48b/IGVFFI9662WYOI.yaml.gz",
"submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/tapseq_seqspec.out.Auxin0hrs-Rep2-S4.rna.yaml.gz",
"upload_status": "validated"
}
],
"input_file_set_for": [
"/analysis-sets/IGVFDS5308EMCG/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 86015c12-b9a6-43ba-9601-5d75aab4d39c was removed from this measurement set.",
"preferred_assay_title": "TAP-seq",
"protocols": [
"https://www.protocols.io/view/crispri-of-regulatory-elements-upon-degron-operati-5jyl82d59l2w/v1"
],
"release_timestamp": "2024-07-10T19:53:28.769965+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0767GJUV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0767GJUV",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_TAPseq-Auxin0hrs-Rep2"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS9869EMNE/",
"accession": "IGVFDS9869EMNE",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting accessible genome regions in 29 genomic loci"
}
],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference"
}
],
"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 modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "21",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-03T19:11:36.315221+00:00",
"summary": "TAP-seq integrating a guide (sgRNA) library targeting accessible genome regions in 29 genomic loci",
"uuid": "26e12241-ab13-4312-9d9c-aa8782baff35"
}