{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6475OLUM/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6475OLUM",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_HTO_LW432"
],
"audit": {
"ERROR": [
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS6475OLUM](/auxiliary-sets/IGVFDS6475OLUM/) has a sequence file [IGVFFI0610DXYU](/sequence-files/IGVFFI0610DXYU/) 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/IGVFDS6475OLUM/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS6475OLUM](/auxiliary-sets/IGVFDS6475OLUM/) has a sequence file [IGVFFI2122JFVV](/sequence-files/IGVFFI2122JFVV/) 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/IGVFDS6475OLUM/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS6475OLUM](/auxiliary-sets/IGVFDS6475OLUM/) has a sequence file [IGVFFI7648FKCT](/sequence-files/IGVFFI7648FKCT/) 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/IGVFDS6475OLUM/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS6475OLUM](/auxiliary-sets/IGVFDS6475OLUM/) has a sequence file [IGVFFI9258ZTXM](/sequence-files/IGVFFI9258ZTXM/) 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/IGVFDS6475OLUM/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6475OLUM](/auxiliary-sets/IGVFDS6475OLUM/) has sequence file(s): [IGVFFI0610DXYU](/sequence-files/IGVFFI0610DXYU/), [IGVFFI2122JFVV](/sequence-files/IGVFFI2122JFVV/), [IGVFFI7648FKCT](/sequence-files/IGVFFI7648FKCT/), [IGVFFI9258ZTXM](/sequence-files/IGVFFI9258ZTXM/) 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/IGVFDS6475OLUM/"
}
]
},
"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": "2024-08-16T20:05:17.040502+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/IGVFFI0610DXYU/",
"accession": "IGVFFI0610DXYU",
"aliases": [
"gary-hon:LW432C_6_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T18:48:35.423797+00:00",
"file_format": "fastq",
"file_size": 508339568,
"href": "/sequence-files/IGVFFI0610DXYU/@@download/IGVFFI0610DXYU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/a909900e-423a-461c-980c-ba66c4868a76/IGVFFI0610DXYU.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//LW432C_S26_L006_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2122JFVV/",
"accession": "IGVFFI2122JFVV",
"aliases": [
"gary-hon:LW432C_6_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T18:48:50.377337+00:00",
"file_format": "fastq",
"file_size": 545085248,
"href": "/sequence-files/IGVFFI2122JFVV/@@download/IGVFFI2122JFVV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/bd2fa977-62c4-487f-82cb-49225ccd4e0b/IGVFFI2122JFVV.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//LW432C_S26_L006_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7648FKCT/",
"accession": "IGVFFI7648FKCT",
"aliases": [
"gary-hon:LW432C_6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T18:49:05.636455+00:00",
"file_format": "fastq",
"file_size": 5250457712,
"href": "/sequence-files/IGVFFI7648FKCT/@@download/IGVFFI7648FKCT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/11ea991e-4bfc-45b1-85be-168bce449608/IGVFFI7648FKCT.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//LW432C_S26_L006_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9258ZTXM/",
"accession": "IGVFFI9258ZTXM",
"aliases": [
"gary-hon:LW432C_6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T18:50:01.735253+00:00",
"file_format": "fastq",
"file_size": 5637295798,
"href": "/sequence-files/IGVFFI9258ZTXM/@@download/IGVFFI9258ZTXM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/4bf7368d-a95a-468b-8687-cd36a47da050/IGVFFI9258ZTXM.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//LW432C_S26_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/IGVFDS8183DTKY/",
"accession": "IGVFDS8183DTKY",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_LW432"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3839SOTK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3839SOTK",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_PB9_LW432"
],
"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_LW432), 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": "2024-11-13T18:48:35.423797+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": "71d58a02-7440-4707-b3bc-850b8327d531"
}