{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8183DTKY/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8183DTKY",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_LW432"
],
"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 [IGVFDS6475OLUM](/auxiliary-sets/IGVFDS6475OLUM/) has a sequence file [IGVFFI0610DXYU](/sequence-files/IGVFFI0610DXYU/) 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/IGVFDS6475OLUM/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS6475OLUM](/auxiliary-sets/IGVFDS6475OLUM/) has a sequence file [IGVFFI2122JFVV](/sequence-files/IGVFFI2122JFVV/) 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/IGVFDS6475OLUM/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS6475OLUM](/auxiliary-sets/IGVFDS6475OLUM/) has a sequence file [IGVFFI7648FKCT](/sequence-files/IGVFFI7648FKCT/) 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/IGVFDS6475OLUM/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS6475OLUM](/auxiliary-sets/IGVFDS6475OLUM/) has a sequence file [IGVFFI9258ZTXM](/sequence-files/IGVFFI9258ZTXM/) 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/IGVFDS6475OLUM/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS5403GYDH](/auxiliary-sets/IGVFDS5403GYDH/) has a sequence file [IGVFFI2639TNEY](/sequence-files/IGVFFI2639TNEY/) 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/IGVFDS5403GYDH/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS5403GYDH](/auxiliary-sets/IGVFDS5403GYDH/) has a sequence file [IGVFFI0508AHMI](/sequence-files/IGVFFI0508AHMI/) 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/IGVFDS5403GYDH/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS5403GYDH](/auxiliary-sets/IGVFDS5403GYDH/) has a sequence file [IGVFFI7827HSIX](/sequence-files/IGVFFI7827HSIX/) 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/IGVFDS5403GYDH/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS5403GYDH](/auxiliary-sets/IGVFDS5403GYDH/) has a sequence file [IGVFFI1627XZSE](/sequence-files/IGVFFI1627XZSE/) 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/IGVFDS5403GYDH/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8183DTKY](/measurement-sets/IGVFDS8183DTKY/) has sequence file(s): [IGVFFI1425SKXL](/sequence-files/IGVFFI1425SKXL/), [IGVFFI0749NOYM](/sequence-files/IGVFFI0749NOYM/), [IGVFFI1896GAGA](/sequence-files/IGVFFI1896GAGA/), [IGVFFI2166QDOO](/sequence-files/IGVFFI2166QDOO/) 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/IGVFDS8183DTKY/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6475OLUM](/auxiliary-sets/IGVFDS6475OLUM/) has sequence file(s): [IGVFFI0610DXYU](/sequence-files/IGVFFI0610DXYU/), [IGVFFI2122JFVV](/sequence-files/IGVFFI2122JFVV/), [IGVFFI7648FKCT](/sequence-files/IGVFFI7648FKCT/), [IGVFFI9258ZTXM](/sequence-files/IGVFFI9258ZTXM/) 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/IGVFDS6475OLUM/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5403GYDH](/auxiliary-sets/IGVFDS5403GYDH/) has sequence file(s): [IGVFFI2639TNEY](/sequence-files/IGVFFI2639TNEY/), [IGVFFI0508AHMI](/sequence-files/IGVFFI0508AHMI/), [IGVFFI7827HSIX](/sequence-files/IGVFFI7827HSIX/), [IGVFFI1627XZSE](/sequence-files/IGVFFI1627XZSE/) 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/IGVFDS5403GYDH/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5403GYDH/",
"accession": "IGVFDS5403GYDH",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_sgRNA_LW432"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6475OLUM/",
"accession": "IGVFDS6475OLUM",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_HTO_LW432"
],
"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": "2024-08-16T20:32:05.618272+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/IGVFFI1425SKXL/",
"accession": "IGVFFI1425SKXL",
"aliases": [
"gary-hon:LW432_5_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:08:02.234500+00:00",
"file_format": "fastq",
"file_size": 2716386912,
"href": "/sequence-files/IGVFFI1425SKXL/@@download/IGVFFI1425SKXL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/d179c1d7-900c-4d41-91be-5e21373cbafd/IGVFFI1425SKXL.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.Hon17_18/scRNA//LW432_S1_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0749NOYM/",
"accession": "IGVFFI0749NOYM",
"aliases": [
"gary-hon:LW432_5_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:09:07.763084+00:00",
"file_format": "fastq",
"file_size": 31554150355,
"href": "/sequence-files/IGVFFI0749NOYM/@@download/IGVFFI0749NOYM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/a27a02d1-cd8f-4989-8ea9-a6e27362ee09/IGVFFI0749NOYM.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.Hon17_18/scRNA//LW432_S1_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1896GAGA/",
"accession": "IGVFFI1896GAGA",
"aliases": [
"gary-hon:LW432_5_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:08:35.652335+00:00",
"file_format": "fastq",
"file_size": 2553564504,
"href": "/sequence-files/IGVFFI1896GAGA/@@download/IGVFFI1896GAGA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/8978da3e-7812-41f1-b92f-604556d2e3b5/IGVFFI1896GAGA.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.Hon17_18/scRNA//LW432_S1_L005_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2166QDOO/",
"accession": "IGVFFI2166QDOO",
"aliases": [
"gary-hon:LW432_5_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:13:52.469112+00:00",
"file_format": "fastq",
"file_size": 31827269670,
"href": "/sequence-files/IGVFFI2166QDOO/@@download/IGVFFI2166QDOO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/7804874d-acdd-4333-95ce-457110397462/IGVFFI2166QDOO.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.Hon17_18/scRNA//LW432_S1_L005_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2266YDVM/"
],
"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/IGVFSM3839SOTK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3839SOTK",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_PB9_LW432"
],
"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_LW432), 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": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-11-13T18:48:35.423797+00:00",
"submitter_comment": "Transcriptiome for LW432",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "a0701133-9f96-49d4-9be2-58c128f40d1f"
}