{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3774FYIW/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3774FYIW",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_HTO_LW433"
],
"audit": {
"ERROR": [
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3774FYIW](/auxiliary-sets/IGVFDS3774FYIW/) has a sequence file [IGVFFI5934NNRV](/sequence-files/IGVFFI5934NNRV/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
"level": 60,
"level_name": "ERROR",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS3774FYIW/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3774FYIW](/auxiliary-sets/IGVFDS3774FYIW/) has a sequence file [IGVFFI5709SYEW](/sequence-files/IGVFFI5709SYEW/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
"level": 60,
"level_name": "ERROR",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS3774FYIW/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3774FYIW](/auxiliary-sets/IGVFDS3774FYIW/) has a sequence file [IGVFFI2279YOXY](/sequence-files/IGVFFI2279YOXY/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
"level": 60,
"level_name": "ERROR",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS3774FYIW/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3774FYIW](/auxiliary-sets/IGVFDS3774FYIW/) has a sequence file [IGVFFI2499JLDM](/sequence-files/IGVFFI2499JLDM/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
"level": 60,
"level_name": "ERROR",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS3774FYIW/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3774FYIW](/auxiliary-sets/IGVFDS3774FYIW/) has sequence file(s): [IGVFFI5934NNRV](/sequence-files/IGVFFI5934NNRV/), [IGVFFI5709SYEW](/sequence-files/IGVFFI5709SYEW/), [IGVFFI2279YOXY](/sequence-files/IGVFFI2279YOXY/), [IGVFFI2499JLDM](/sequence-files/IGVFFI2499JLDM/) 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/IGVFDS3774FYIW/"
}
]
},
"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": "2024-08-16T20:05:18.940488+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2718IDDQ/",
"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "cell hashing barcode sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI5934NNRV/",
"accession": "IGVFFI5934NNRV",
"aliases": [
"gary-hon:LW433C_6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T18:51:30.273496+00:00",
"file_format": "fastq",
"file_size": 5218419786,
"href": "/sequence-files/IGVFFI5934NNRV/@@download/IGVFFI5934NNRV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/44982ee3-a323-4c33-a1bc-c797ac6a46bc/IGVFFI5934NNRV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/HTO//LW433C_S27_L006_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5709SYEW/",
"accession": "IGVFFI5709SYEW",
"aliases": [
"gary-hon:LW433C_6_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T18:51:01.357866+00:00",
"file_format": "fastq",
"file_size": 532716527,
"href": "/sequence-files/IGVFFI5709SYEW/@@download/IGVFFI5709SYEW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/310478a3-c6ff-4b59-a0e1-970dce5ae20f/IGVFFI5709SYEW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/HTO//LW433C_S27_L006_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2279YOXY/",
"accession": "IGVFFI2279YOXY",
"aliases": [
"gary-hon:LW433C_6_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T18:51:15.517375+00:00",
"file_format": "fastq",
"file_size": 618082639,
"href": "/sequence-files/IGVFFI2279YOXY/@@download/IGVFFI2279YOXY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/453f553a-7efb-4fd0-834c-08e99ab1b645/IGVFFI2279YOXY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/HTO//LW433C_S27_L006_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2499JLDM/",
"accession": "IGVFFI2499JLDM",
"aliases": [
"gary-hon:LW433C_6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T18:52:25.203032+00:00",
"file_format": "fastq",
"file_size": 5484936702,
"href": "/sequence-files/IGVFFI2499JLDM/@@download/IGVFFI2499JLDM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/d875c28f-390e-46dc-adb6-d367667d57dd/IGVFFI2499JLDM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008637/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/HTO//LW433C_S27_L006_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2266YDVM/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS8751LXWJ/",
"accession": "IGVFDS8751LXWJ",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_LW433"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1513DHGW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1513DHGW",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_PB9_LW433"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS0346MQBH/"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0003045/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H9"
],
"status": "released",
"summary": "H9",
"term_name": "H9"
}
],
"status": "preview",
"summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW433), female, 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": "2024-11-13T18:51:01.357866+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": "c149c32e-f239-4c8c-9613-27cf9f2cacd7"
}