{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4121IORO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4121IORO",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_LW422"
],
"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 [IGVFDS0170TMBA](/auxiliary-sets/IGVFDS0170TMBA/) has a sequence file [IGVFFI0648VXAD](/sequence-files/IGVFFI0648VXAD/) 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/IGVFDS0170TMBA/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS0170TMBA](/auxiliary-sets/IGVFDS0170TMBA/) has a sequence file [IGVFFI6422IECE](/sequence-files/IGVFFI6422IECE/) 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/IGVFDS0170TMBA/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS0170TMBA](/auxiliary-sets/IGVFDS0170TMBA/) has a sequence file [IGVFFI2319YGLG](/sequence-files/IGVFFI2319YGLG/) 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/IGVFDS0170TMBA/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS0170TMBA](/auxiliary-sets/IGVFDS0170TMBA/) has a sequence file [IGVFFI2369OANJ](/sequence-files/IGVFFI2369OANJ/) 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/IGVFDS0170TMBA/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS1760WHSE](/auxiliary-sets/IGVFDS1760WHSE/) has a sequence file [IGVFFI7174BBBZ](/sequence-files/IGVFFI7174BBBZ/) 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/IGVFDS1760WHSE/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS1760WHSE](/auxiliary-sets/IGVFDS1760WHSE/) has a sequence file [IGVFFI5590FVKN](/sequence-files/IGVFFI5590FVKN/) 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/IGVFDS1760WHSE/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS1760WHSE](/auxiliary-sets/IGVFDS1760WHSE/) has a sequence file [IGVFFI9985DIGI](/sequence-files/IGVFFI9985DIGI/) 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/IGVFDS1760WHSE/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS1760WHSE](/auxiliary-sets/IGVFDS1760WHSE/) has a sequence file [IGVFFI7072KBGQ](/sequence-files/IGVFFI7072KBGQ/) 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/IGVFDS1760WHSE/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4121IORO](/measurement-sets/IGVFDS4121IORO/) has sequence file(s): [IGVFFI3229RCYO](/sequence-files/IGVFFI3229RCYO/), [IGVFFI3498KXVK](/sequence-files/IGVFFI3498KXVK/), [IGVFFI4735OYGD](/sequence-files/IGVFFI4735OYGD/), [IGVFFI1429SPMA](/sequence-files/IGVFFI1429SPMA/) 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/IGVFDS4121IORO/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0170TMBA](/auxiliary-sets/IGVFDS0170TMBA/) has sequence file(s): [IGVFFI0648VXAD](/sequence-files/IGVFFI0648VXAD/), [IGVFFI6422IECE](/sequence-files/IGVFFI6422IECE/), [IGVFFI2319YGLG](/sequence-files/IGVFFI2319YGLG/), [IGVFFI2369OANJ](/sequence-files/IGVFFI2369OANJ/) 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/IGVFDS0170TMBA/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1760WHSE](/auxiliary-sets/IGVFDS1760WHSE/) has sequence file(s): [IGVFFI7174BBBZ](/sequence-files/IGVFFI7174BBBZ/), [IGVFFI5590FVKN](/sequence-files/IGVFFI5590FVKN/), [IGVFFI9985DIGI](/sequence-files/IGVFFI9985DIGI/), [IGVFFI7072KBGQ](/sequence-files/IGVFFI7072KBGQ/) 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/IGVFDS1760WHSE/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0170TMBA/",
"accession": "IGVFDS0170TMBA",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_sgRNA_LW422"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS1760WHSE/",
"accession": "IGVFDS1760WHSE",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_HTO_LW422"
],
"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": "2024-08-16T20:31:46.375605+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/IGVFFI3229RCYO/",
"accession": "IGVFFI3229RCYO",
"aliases": [
"gary-hon:LW422_7_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:10:59.772029+00:00",
"file_format": "fastq",
"file_size": 1923706635,
"href": "/sequence-files/IGVFFI3229RCYO/@@download/IGVFFI3229RCYO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/a466d434-a282-4556-ad33-2316a1d8767e/IGVFFI3229RCYO.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//LW422_S47_L007_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3498KXVK/",
"accession": "IGVFFI3498KXVK",
"aliases": [
"gary-hon:LW422_7_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:15:16.018557+00:00",
"file_format": "fastq",
"file_size": 24020772630,
"href": "/sequence-files/IGVFFI3498KXVK/@@download/IGVFFI3498KXVK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/d449567b-3417-4ad0-862a-75fcd7d99b0a/IGVFFI3498KXVK.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//LW422_S47_L007_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4735OYGD/",
"accession": "IGVFFI4735OYGD",
"aliases": [
"gary-hon:LW422_7_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:11:26.529997+00:00",
"file_format": "fastq",
"file_size": 25648944227,
"href": "/sequence-files/IGVFFI4735OYGD/@@download/IGVFFI4735OYGD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/33a5a524-5198-4e27-9f6f-27e283f66995/IGVFFI4735OYGD.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//LW422_S47_L007_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1429SPMA/",
"accession": "IGVFFI1429SPMA",
"aliases": [
"gary-hon:LW422_7_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:10:34.117909+00:00",
"file_format": "fastq",
"file_size": 1860298431,
"href": "/sequence-files/IGVFFI1429SPMA/@@download/IGVFFI1429SPMA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/c160017e-647b-4542-8cfd-953e088f2b14/IGVFFI1429SPMA.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//LW422_S47_L007_I1_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/IGVFSM8986CPUS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8986CPUS",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_Inducible_LW422"
],
"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_LW422), 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": "2024-11-13T20:57:25.764962+00:00",
"submitter_comment": "Transcriptiome for LW422",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "a6a73cbd-facb-4ca4-bf0a-77586a7628a5"
}