{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2406OSFC/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2406OSFC",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW237"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2406OSFC](/auxiliary-sets/IGVFDS2406OSFC/) has sequence file(s) [IGVFFI4271ZYNK](/sequence-files/IGVFFI4271ZYNK/), [IGVFFI4753ESNB](/sequence-files/IGVFFI4753ESNB/), [IGVFFI7543WDMT](/sequence-files/IGVFFI7543WDMT/), [IGVFFI6111FHSJ](/sequence-files/IGVFFI6111FHSJ/), [IGVFFI0561MNSA](/sequence-files/IGVFFI0561MNSA/), [IGVFFI9370EAFR](/sequence-files/IGVFFI9370EAFR/), [IGVFFI7058PKFB](/sequence-files/IGVFFI7058PKFB/), [IGVFFI3224UVDH](/sequence-files/IGVFFI3224UVDH/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS2406OSFC/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2406OSFC](/auxiliary-sets/IGVFDS2406OSFC/) has sequence file(s): [IGVFFI4271ZYNK](/sequence-files/IGVFFI4271ZYNK/), [IGVFFI4753ESNB](/sequence-files/IGVFFI4753ESNB/), [IGVFFI7543WDMT](/sequence-files/IGVFFI7543WDMT/), [IGVFFI6111FHSJ](/sequence-files/IGVFFI6111FHSJ/), [IGVFFI0561MNSA](/sequence-files/IGVFFI0561MNSA/), [IGVFFI9370EAFR](/sequence-files/IGVFFI9370EAFR/), [IGVFFI7058PKFB](/sequence-files/IGVFFI7058PKFB/), [IGVFFI3224UVDH](/sequence-files/IGVFFI3224UVDH/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS2406OSFC/"
}
]
},
"award": {
"@id": "/awards/HG011996/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/95d84f03-8ce0-489c-a755-f33ced139c5d/",
"title": "Gary Hon"
},
"title": "Multiscale functional characterization of genomic variation in human developmental disorders"
},
"control_for": [],
"creation_timestamp": "2024-02-15T23:35:44.927615+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "cell hashing barcode sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI4271ZYNK/",
"accession": "IGVFFI4271ZYNK",
"aliases": [
"gary-hon:LW237C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:33:19.889855+00:00",
"file_format": "fastq",
"file_size": 116890177,
"href": "/sequence-files/IGVFFI4271ZYNK/@@download/IGVFFI4271ZYNK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/927a3650-2054-4692-90a2-719b21d7208a/IGVFFI4271ZYNK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW237C_S15_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4753ESNB/",
"accession": "IGVFFI4753ESNB",
"aliases": [
"gary-hon:LW237C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:33:25.168299+00:00",
"file_format": "fastq",
"file_size": 348542485,
"href": "/sequence-files/IGVFFI4753ESNB/@@download/IGVFFI4753ESNB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/f23ef4e1-2a31-4dff-ae60-600cf9b6e49e/IGVFFI4753ESNB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW237C_S15_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7543WDMT/",
"accession": "IGVFFI7543WDMT",
"aliases": [
"gary-hon:LW237C_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:34:01.968392+00:00",
"file_format": "fastq",
"file_size": 577035525,
"href": "/sequence-files/IGVFFI7543WDMT/@@download/IGVFFI7543WDMT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/098ceee1-c429-4686-9158-83ebd9abd5b9/IGVFFI7543WDMT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW237C_S15_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6111FHSJ/",
"accession": "IGVFFI6111FHSJ",
"aliases": [
"gary-hon:LW237C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:33:14.745156+00:00",
"file_format": "fastq",
"file_size": 101042599,
"href": "/sequence-files/IGVFFI6111FHSJ/@@download/IGVFFI6111FHSJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/c243f120-74d0-4cd9-b98e-3fa00e01a694/IGVFFI6111FHSJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW237C_S15_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0561MNSA/",
"accession": "IGVFFI0561MNSA",
"aliases": [
"gary-hon:LW237C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:33:32.378083+00:00",
"file_format": "fastq",
"file_size": 637913684,
"href": "/sequence-files/IGVFFI0561MNSA/@@download/IGVFFI0561MNSA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/8699a507-87ec-44dd-895f-e7327bcf5973/IGVFFI0561MNSA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW237C_S15_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9370EAFR/",
"accession": "IGVFFI9370EAFR",
"aliases": [
"gary-hon:LW237C_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:33:55.076596+00:00",
"file_format": "fastq",
"file_size": 316639582,
"href": "/sequence-files/IGVFFI9370EAFR/@@download/IGVFFI9370EAFR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/3de02df0-89fa-44b8-a21a-1e8afb8d2f8a/IGVFFI9370EAFR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW237C_S15_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7058PKFB/",
"accession": "IGVFFI7058PKFB",
"aliases": [
"gary-hon:LW237C_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:33:42.208132+00:00",
"file_format": "fastq",
"file_size": 95751941,
"href": "/sequence-files/IGVFFI7058PKFB/@@download/IGVFFI7058PKFB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/0c631d32-8189-4a62-99fb-527dd0b86722/IGVFFI7058PKFB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW237C_S15_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3224UVDH/",
"accession": "IGVFFI3224UVDH",
"aliases": [
"gary-hon:LW237C_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:33:49.552543+00:00",
"file_format": "fastq",
"file_size": 107617912,
"href": "/sequence-files/IGVFFI3224UVDH/@@download/IGVFFI3224UVDH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/7544db04-5586-4059-b77f-abc6f27b1e9e/IGVFFI3224UVDH.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW237C_S15_L002_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9192YMGI/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2593KURF/",
"accession": "IGVFDS2593KURF",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW237"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"notes": "File_set_type enum cell hashing has been renamed to be cell hashing barcode sequencing.",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2329UXLZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2329UXLZ",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW237"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW267), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-02-21T18:33:14.745156+00:00",
"summary": "cell hashing barcode sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "01dba293-16a9-48a1-9ed7-e822077674fb"
}