{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1182KBMU/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1182KBMU",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_sgRNA_LW431"
],
"audit": {
"ERROR": [
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS1182KBMU](/auxiliary-sets/IGVFDS1182KBMU/) has a sequence file [IGVFFI6583VNDG](/sequence-files/IGVFFI6583VNDG/) 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/IGVFDS1182KBMU/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS1182KBMU](/auxiliary-sets/IGVFDS1182KBMU/) has a sequence file [IGVFFI9145LELN](/sequence-files/IGVFFI9145LELN/) 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/IGVFDS1182KBMU/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS1182KBMU](/auxiliary-sets/IGVFDS1182KBMU/) has a sequence file [IGVFFI1005GDSX](/sequence-files/IGVFFI1005GDSX/) 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/IGVFDS1182KBMU/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS1182KBMU](/auxiliary-sets/IGVFDS1182KBMU/) has a sequence file [IGVFFI0606VNOW](/sequence-files/IGVFFI0606VNOW/) 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/IGVFDS1182KBMU/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1182KBMU](/auxiliary-sets/IGVFDS1182KBMU/) has sequence file(s): [IGVFFI6583VNDG](/sequence-files/IGVFFI6583VNDG/), [IGVFFI9145LELN](/sequence-files/IGVFFI9145LELN/), [IGVFFI1005GDSX](/sequence-files/IGVFFI1005GDSX/), [IGVFFI0606VNOW](/sequence-files/IGVFFI0606VNOW/) 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/IGVFDS1182KBMU/"
}
]
},
"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": "2024-08-16T20:05:14.344053+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/IGVFFI6583VNDG/",
"accession": "IGVFFI6583VNDG",
"aliases": [
"gary-hon:LW431B_6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:43:40.075407+00:00",
"file_format": "fastq",
"file_size": 7713142752,
"href": "/sequence-files/IGVFFI6583VNDG/@@download/IGVFFI6583VNDG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/b0d7068a-acb5-4e25-a680-2e2149b848a4/IGVFFI6583VNDG.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//LW431B_S5_L006_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9145LELN/",
"accession": "IGVFFI9145LELN",
"aliases": [
"gary-hon:LW431B_6_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:43:05.302696+00:00",
"file_format": "fastq",
"file_size": 945590903,
"href": "/sequence-files/IGVFFI9145LELN/@@download/IGVFFI9145LELN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/52adf5bc-b32b-411d-8ce8-4b1d5e67d23e/IGVFFI9145LELN.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//LW431B_S5_L006_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1005GDSX/",
"accession": "IGVFFI1005GDSX",
"aliases": [
"gary-hon:LW431B_6_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:43:23.797884+00:00",
"file_format": "fastq",
"file_size": 878192324,
"href": "/sequence-files/IGVFFI1005GDSX/@@download/IGVFFI1005GDSX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/8423a49f-e523-4304-a7c8-4d9c0a134dee/IGVFFI1005GDSX.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//LW431B_S5_L006_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0606VNOW/",
"accession": "IGVFFI0606VNOW",
"aliases": [
"gary-hon:LW431B_6_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:44:56.121179+00:00",
"file_format": "fastq",
"file_size": 7747645287,
"href": "/sequence-files/IGVFFI0606VNOW/@@download/IGVFFI0606VNOW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/25483727-c4c4-48fc-93b1-588ae538bf6a/IGVFFI0606VNOW.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//LW431B_S5_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/IGVFDS5502LTCL/",
"accession": "IGVFDS5502LTCL",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_LW431"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5829AVCL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5829AVCL",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_PB9_LW431"
],
"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_LW431), 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": "2024-11-13T19:43:05.302696+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "a5b3fc1c-9277-485b-ae68-ac6ff580a4e8"
}