{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0922ZREC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0922ZREC",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_LW421"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003660/",
"status": "released",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"audit": {
"ERROR": [
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS6534GRPN](/auxiliary-sets/IGVFDS6534GRPN/) has a sequence file [IGVFFI2506NTEK](/sequence-files/IGVFFI2506NTEK/) 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/IGVFDS6534GRPN/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS6534GRPN](/auxiliary-sets/IGVFDS6534GRPN/) has a sequence file [IGVFFI9611JSKK](/sequence-files/IGVFFI9611JSKK/) 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/IGVFDS6534GRPN/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS6534GRPN](/auxiliary-sets/IGVFDS6534GRPN/) has a sequence file [IGVFFI8979FIEF](/sequence-files/IGVFFI8979FIEF/) 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/IGVFDS6534GRPN/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS6534GRPN](/auxiliary-sets/IGVFDS6534GRPN/) has a sequence file [IGVFFI7778RGQZ](/sequence-files/IGVFFI7778RGQZ/) 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/IGVFDS6534GRPN/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS6780UKAY](/auxiliary-sets/IGVFDS6780UKAY/) has a sequence file [IGVFFI6823TGWS](/sequence-files/IGVFFI6823TGWS/) 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/IGVFDS6780UKAY/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS6780UKAY](/auxiliary-sets/IGVFDS6780UKAY/) has a sequence file [IGVFFI4252WJOM](/sequence-files/IGVFFI4252WJOM/) 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/IGVFDS6780UKAY/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS6780UKAY](/auxiliary-sets/IGVFDS6780UKAY/) has a sequence file [IGVFFI7464YZLJ](/sequence-files/IGVFFI7464YZLJ/) 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/IGVFDS6780UKAY/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS6780UKAY](/auxiliary-sets/IGVFDS6780UKAY/) has a sequence file [IGVFFI5758ILZG](/sequence-files/IGVFFI5758ILZG/) 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/IGVFDS6780UKAY/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6534GRPN](/auxiliary-sets/IGVFDS6534GRPN/) has sequence file(s): [IGVFFI2506NTEK](/sequence-files/IGVFFI2506NTEK/), [IGVFFI9611JSKK](/sequence-files/IGVFFI9611JSKK/), [IGVFFI8979FIEF](/sequence-files/IGVFFI8979FIEF/), [IGVFFI7778RGQZ](/sequence-files/IGVFFI7778RGQZ/) 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/IGVFDS6534GRPN/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0922ZREC](/measurement-sets/IGVFDS0922ZREC/) has sequence file(s): [IGVFFI1593TBSS](/sequence-files/IGVFFI1593TBSS/), [IGVFFI8829FXFG](/sequence-files/IGVFFI8829FXFG/), [IGVFFI5216SPWD](/sequence-files/IGVFFI5216SPWD/), [IGVFFI7835NHIA](/sequence-files/IGVFFI7835NHIA/) 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": "/measurement-sets/IGVFDS0922ZREC/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6780UKAY](/auxiliary-sets/IGVFDS6780UKAY/) has sequence file(s): [IGVFFI6823TGWS](/sequence-files/IGVFFI6823TGWS/), [IGVFFI4252WJOM](/sequence-files/IGVFFI4252WJOM/), [IGVFFI7464YZLJ](/sequence-files/IGVFFI7464YZLJ/), [IGVFFI5758ILZG](/sequence-files/IGVFFI5758ILZG/) 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/IGVFDS6780UKAY/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6534GRPN/",
"accession": "IGVFDS6534GRPN",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_sgRNA_LW421"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6780UKAY/",
"accession": "IGVFDS6780UKAY",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_HTO_LW421"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
}
],
"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": "2024-08-16T20:31:44.181014+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2718IDDQ/",
"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI1593TBSS/",
"accession": "IGVFFI1593TBSS",
"aliases": [
"gary-hon:LW421_7_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:03:12.470579+00:00",
"file_format": "fastq",
"file_size": 1821689415,
"href": "/sequence-files/IGVFFI1593TBSS/@@download/IGVFFI1593TBSS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/4c84f230-fce9-4eaf-917e-e9a568f5f8eb/IGVFFI1593TBSS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/scRNA//LW421_S46_L007_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8829FXFG/",
"accession": "IGVFFI8829FXFG",
"aliases": [
"gary-hon:LW421_7_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:04:02.406956+00:00",
"file_format": "fastq",
"file_size": 22477997060,
"href": "/sequence-files/IGVFFI8829FXFG/@@download/IGVFFI8829FXFG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/b087258e-cfb3-4c74-b81c-5859918012fe/IGVFFI8829FXFG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/scRNA//LW421_S46_L007_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5216SPWD/",
"accession": "IGVFFI5216SPWD",
"aliases": [
"gary-hon:LW421_7_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:03:37.992240+00:00",
"file_format": "fastq",
"file_size": 1686268057,
"href": "/sequence-files/IGVFFI5216SPWD/@@download/IGVFFI5216SPWD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/672a445b-c61a-4aab-b8d4-77476661c608/IGVFFI5216SPWD.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/scRNA//LW421_S46_L007_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7835NHIA/",
"accession": "IGVFFI7835NHIA",
"aliases": [
"gary-hon:LW421_7_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:07:24.256333+00:00",
"file_format": "fastq",
"file_size": 20962569163,
"href": "/sequence-files/IGVFFI7835NHIA/@@download/IGVFFI7835NHIA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/99082deb-3c5d-4bbf-bb32-8fd2ebb31155/IGVFFI7835NHIA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/scRNA//LW421_S46_L007_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS6924DJAZ/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"preferred_assay_title": "Perturb-seq",
"protocols": [
"https://www.protocols.io/view/experimental-procedures-for-tf-perturb-seq-ut-sout-denf3dbn"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3680SAKS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3680SAKS",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_Inducible_LW421"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS0346MQBH/",
"accession": "IGVFDS0346MQBH",
"file_set_type": "guide library",
"status": "preview",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"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_LW421), 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": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-11-13T20:55:08.043354+00:00",
"submitter_comment": "Transcriptiome for LW421",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "8dd75ce5-c8c5-4e4b-b336-bfaa59048ce0"
}