{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1340IBKW/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1340IBKW",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_HTO_LW434"
],
"audit": {
"ERROR": [
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS1340IBKW](/auxiliary-sets/IGVFDS1340IBKW/) has a sequence file [IGVFFI3780WHTV](/sequence-files/IGVFFI3780WHTV/) 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/IGVFDS1340IBKW/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS1340IBKW](/auxiliary-sets/IGVFDS1340IBKW/) has a sequence file [IGVFFI2537MGAU](/sequence-files/IGVFFI2537MGAU/) 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/IGVFDS1340IBKW/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS1340IBKW](/auxiliary-sets/IGVFDS1340IBKW/) has a sequence file [IGVFFI0210CMIS](/sequence-files/IGVFFI0210CMIS/) 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/IGVFDS1340IBKW/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS1340IBKW](/auxiliary-sets/IGVFDS1340IBKW/) has a sequence file [IGVFFI3021FRGV](/sequence-files/IGVFFI3021FRGV/) 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/IGVFDS1340IBKW/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1340IBKW](/auxiliary-sets/IGVFDS1340IBKW/) has sequence file(s): [IGVFFI3780WHTV](/sequence-files/IGVFFI3780WHTV/), [IGVFFI2537MGAU](/sequence-files/IGVFFI2537MGAU/), [IGVFFI0210CMIS](/sequence-files/IGVFFI0210CMIS/), [IGVFFI3021FRGV](/sequence-files/IGVFFI3021FRGV/) 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/IGVFDS1340IBKW/"
}
]
},
"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": "2024-08-16T20:05:20.788028+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/IGVFFI3780WHTV/",
"accession": "IGVFFI3780WHTV",
"aliases": [
"gary-hon:LW434C_6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T18:54:41.295246+00:00",
"file_format": "fastq",
"file_size": 4791764844,
"href": "/sequence-files/IGVFFI3780WHTV/@@download/IGVFFI3780WHTV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/fb7e0f5f-4f56-42af-9c6a-34d8a1a673c1/IGVFFI3780WHTV.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//LW434C_S28_L006_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2537MGAU/",
"accession": "IGVFFI2537MGAU",
"aliases": [
"gary-hon:LW434C_6_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T18:53:24.348008+00:00",
"file_format": "fastq",
"file_size": 462461387,
"href": "/sequence-files/IGVFFI2537MGAU/@@download/IGVFFI2537MGAU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/e77c2500-afb3-4eac-a32f-5d35eeeba771/IGVFFI2537MGAU.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//LW434C_S28_L006_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0210CMIS/",
"accession": "IGVFFI0210CMIS",
"aliases": [
"gary-hon:LW434C_6_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T18:53:37.586484+00:00",
"file_format": "fastq",
"file_size": 480596730,
"href": "/sequence-files/IGVFFI0210CMIS/@@download/IGVFFI0210CMIS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/21cdb82a-9ac8-4e81-ae6f-5b006737ba41/IGVFFI0210CMIS.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//LW434C_S28_L006_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3021FRGV/",
"accession": "IGVFFI3021FRGV",
"aliases": [
"gary-hon:LW434C_6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T18:53:52.078224+00:00",
"file_format": "fastq",
"file_size": 4541567343,
"href": "/sequence-files/IGVFFI3021FRGV/@@download/IGVFFI3021FRGV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/c3f962fe-8ff3-465a-906a-cdde8a1af8e8/IGVFFI3021FRGV.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//LW434C_S28_L006_R1_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/IGVFDS7288IQLC/",
"accession": "IGVFDS7288IQLC",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_LW434"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8133YEXK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8133YEXK",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_PB9_LW434"
],
"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_LW434), 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": "2024-11-13T18:53:24.348008+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": "aa4c1e3f-50bd-4816-aa02-f44e0c8fa878"
}