{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5986XHYV/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5986XHYV",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW231"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5986XHYV](/auxiliary-sets/IGVFDS5986XHYV/) has sequence file(s) [IGVFFI1563TIUE](/sequence-files/IGVFFI1563TIUE/), [IGVFFI4146MFBE](/sequence-files/IGVFFI4146MFBE/), [IGVFFI4745WZDI](/sequence-files/IGVFFI4745WZDI/), [IGVFFI0503LCOS](/sequence-files/IGVFFI0503LCOS/), [IGVFFI8165EFZM](/sequence-files/IGVFFI8165EFZM/), [IGVFFI2505NLLH](/sequence-files/IGVFFI2505NLLH/), [IGVFFI5897DBBP](/sequence-files/IGVFFI5897DBBP/), [IGVFFI3760ZTYQ](/sequence-files/IGVFFI3760ZTYQ/) 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/IGVFDS5986XHYV/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5986XHYV](/auxiliary-sets/IGVFDS5986XHYV/) has sequence file(s): [IGVFFI1563TIUE](/sequence-files/IGVFFI1563TIUE/), [IGVFFI4146MFBE](/sequence-files/IGVFFI4146MFBE/), [IGVFFI4745WZDI](/sequence-files/IGVFFI4745WZDI/), [IGVFFI0503LCOS](/sequence-files/IGVFFI0503LCOS/), [IGVFFI8165EFZM](/sequence-files/IGVFFI8165EFZM/), [IGVFFI2505NLLH](/sequence-files/IGVFFI2505NLLH/), [IGVFFI5897DBBP](/sequence-files/IGVFFI5897DBBP/), [IGVFFI3760ZTYQ](/sequence-files/IGVFFI3760ZTYQ/) 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/IGVFDS5986XHYV/"
}
]
},
"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": "2024-02-15T23:35:31.063571+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/IGVFFI1563TIUE/",
"accession": "IGVFFI1563TIUE",
"aliases": [
"gary-hon:LW231C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:18:39.247678+00:00",
"file_format": "fastq",
"file_size": 133366421,
"href": "/sequence-files/IGVFFI1563TIUE/@@download/IGVFFI1563TIUE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/e914106c-f121-4649-ba17-58cd2f7cbd7f/IGVFFI1563TIUE.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/LW231C_S9_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4146MFBE/",
"accession": "IGVFFI4146MFBE",
"aliases": [
"gary-hon:LW231C_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:19:20.376071+00:00",
"file_format": "fastq",
"file_size": 372292508,
"href": "/sequence-files/IGVFFI4146MFBE/@@download/IGVFFI4146MFBE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/fd042069-2be6-491f-acdd-0e2443628d75/IGVFFI4146MFBE.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/LW231C_S9_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4745WZDI/",
"accession": "IGVFFI4745WZDI",
"aliases": [
"gary-hon:LW231C_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:19:27.750712+00:00",
"file_format": "fastq",
"file_size": 684686257,
"href": "/sequence-files/IGVFFI4745WZDI/@@download/IGVFFI4745WZDI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/92cc6917-e72d-4cb7-9582-359ce00e31ba/IGVFFI4745WZDI.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/LW231C_S9_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0503LCOS/",
"accession": "IGVFFI0503LCOS",
"aliases": [
"gary-hon:LW231C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:18:34.056584+00:00",
"file_format": "fastq",
"file_size": 137138351,
"href": "/sequence-files/IGVFFI0503LCOS/@@download/IGVFFI0503LCOS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/f1f3c05f-06f7-4760-a513-7c5adab2e551/IGVFFI0503LCOS.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/LW231C_S9_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8165EFZM/",
"accession": "IGVFFI8165EFZM",
"aliases": [
"gary-hon:LW231C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:18:44.474432+00:00",
"file_format": "fastq",
"file_size": 407573232,
"href": "/sequence-files/IGVFFI8165EFZM/@@download/IGVFFI8165EFZM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/ee7659b3-483e-46d1-ae8e-452797b1635f/IGVFFI8165EFZM.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/LW231C_S9_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2505NLLH/",
"accession": "IGVFFI2505NLLH",
"aliases": [
"gary-hon:LW231C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:18:53.393992+00:00",
"file_format": "fastq",
"file_size": 752498667,
"href": "/sequence-files/IGVFFI2505NLLH/@@download/IGVFFI2505NLLH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/298de2e7-5753-466f-91ba-e9f6dddb13a0/IGVFFI2505NLLH.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/LW231C_S9_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5897DBBP/",
"accession": "IGVFFI5897DBBP",
"aliases": [
"gary-hon:LW231C_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:19:03.686424+00:00",
"file_format": "fastq",
"file_size": 129440361,
"href": "/sequence-files/IGVFFI5897DBBP/@@download/IGVFFI5897DBBP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/e5a5aed3-6ca2-4be0-a197-725675fd6791/IGVFFI5897DBBP.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/LW231C_S9_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3760ZTYQ/",
"accession": "IGVFFI3760ZTYQ",
"aliases": [
"gary-hon:LW231C_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:19:13.991594+00:00",
"file_format": "fastq",
"file_size": 118454436,
"href": "/sequence-files/IGVFFI3760ZTYQ/@@download/IGVFFI3760ZTYQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/c92b4b0e-bb79-4c03-a943-434e5ea99840/IGVFFI3760ZTYQ.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/LW231C_S9_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/IGVFDS1334EIHS/",
"accession": "IGVFDS1334EIHS",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW231"
],
"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/IGVFSM7740VKXC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7740VKXC",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW231"
],
"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_LW261), 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": "2024-02-21T18:18:34.056584+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": "010e6b72-f5a0-423f-9c5d-cfe8165a220f"
}