{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS9735REPA/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS9735REPA",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_sgRNA_LW423"
],
"audit": {
"ERROR": [
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS9735REPA](/auxiliary-sets/IGVFDS9735REPA/) has a sequence file [IGVFFI1024SNXF](/sequence-files/IGVFFI1024SNXF/) 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/IGVFDS9735REPA/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS9735REPA](/auxiliary-sets/IGVFDS9735REPA/) has a sequence file [IGVFFI8917IMMW](/sequence-files/IGVFFI8917IMMW/) 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/IGVFDS9735REPA/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS9735REPA](/auxiliary-sets/IGVFDS9735REPA/) has a sequence file [IGVFFI1900TGMR](/sequence-files/IGVFFI1900TGMR/) 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/IGVFDS9735REPA/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS9735REPA](/auxiliary-sets/IGVFDS9735REPA/) has a sequence file [IGVFFI3207RGMA](/sequence-files/IGVFFI3207RGMA/) 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/IGVFDS9735REPA/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9735REPA](/auxiliary-sets/IGVFDS9735REPA/) has sequence file(s): [IGVFFI1024SNXF](/sequence-files/IGVFFI1024SNXF/), [IGVFFI8917IMMW](/sequence-files/IGVFFI8917IMMW/), [IGVFFI1900TGMR](/sequence-files/IGVFFI1900TGMR/), [IGVFFI3207RGMA](/sequence-files/IGVFFI3207RGMA/) 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/IGVFDS9735REPA/"
}
]
},
"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": "2024-08-16T20:04:59.919588+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2718IDDQ/",
"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI1024SNXF/",
"accession": "IGVFFI1024SNXF",
"aliases": [
"gary-hon:LW423B_6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:45:01.118512+00:00",
"file_format": "fastq",
"file_size": 7847489637,
"href": "/sequence-files/IGVFFI1024SNXF/@@download/IGVFFI1024SNXF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/afbf65d6-f98f-46e9-ac41-03555cf4d35c/IGVFFI1024SNXF.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/sgRNA//LW423B_S3_L006_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8917IMMW/",
"accession": "IGVFFI8917IMMW",
"aliases": [
"gary-hon:LW423B_6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:46:18.907871+00:00",
"file_format": "fastq",
"file_size": 7902236882,
"href": "/sequence-files/IGVFFI8917IMMW/@@download/IGVFFI8917IMMW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/c2d74850-26d4-4319-9f6c-e86b992806b6/IGVFFI8917IMMW.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/sgRNA//LW423B_S3_L006_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1900TGMR/",
"accession": "IGVFFI1900TGMR",
"aliases": [
"gary-hon:LW423B_6_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:44:24.979692+00:00",
"file_format": "fastq",
"file_size": 873850387,
"href": "/sequence-files/IGVFFI1900TGMR/@@download/IGVFFI1900TGMR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/fcd8da68-c48c-49f2-a92a-ce3153c09587/IGVFFI1900TGMR.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/sgRNA//LW423B_S3_L006_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3207RGMA/",
"accession": "IGVFFI3207RGMA",
"aliases": [
"gary-hon:LW423B_6_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:44:42.313126+00:00",
"file_format": "fastq",
"file_size": 900642087,
"href": "/sequence-files/IGVFFI3207RGMA/@@download/IGVFFI3207RGMA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/4c2f5d54-99a6-42b7-bff2-d51ee43e22f8/IGVFFI3207RGMA.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/sgRNA//LW423B_S3_L006_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6924DJAZ/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS3847PDAQ/",
"accession": "IGVFDS3847PDAQ",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_LW423"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3015ZQZL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3015ZQZL",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_Inducible_LW423"
],
"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_LW423), female, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) 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": "2024-11-13T21:44:24.979692+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "86bab212-98a3-400c-9c37-750e8ce71d3d"
}