{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8751LXWJ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8751LXWJ",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_LW433"
],
"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 [IGVFDS3919NBFE](/auxiliary-sets/IGVFDS3919NBFE/) has a sequence file [IGVFFI5800QJKD](/sequence-files/IGVFFI5800QJKD/) 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/IGVFDS3919NBFE/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3919NBFE](/auxiliary-sets/IGVFDS3919NBFE/) has a sequence file [IGVFFI7530AEJH](/sequence-files/IGVFFI7530AEJH/) 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/IGVFDS3919NBFE/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3919NBFE](/auxiliary-sets/IGVFDS3919NBFE/) has a sequence file [IGVFFI5201BBTZ](/sequence-files/IGVFFI5201BBTZ/) 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/IGVFDS3919NBFE/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3919NBFE](/auxiliary-sets/IGVFDS3919NBFE/) has a sequence file [IGVFFI5561SSLS](/sequence-files/IGVFFI5561SSLS/) 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/IGVFDS3919NBFE/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3774FYIW](/auxiliary-sets/IGVFDS3774FYIW/) has a sequence file [IGVFFI5934NNRV](/sequence-files/IGVFFI5934NNRV/) 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/IGVFDS3774FYIW/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3774FYIW](/auxiliary-sets/IGVFDS3774FYIW/) has a sequence file [IGVFFI5709SYEW](/sequence-files/IGVFFI5709SYEW/) 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/IGVFDS3774FYIW/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3774FYIW](/auxiliary-sets/IGVFDS3774FYIW/) has a sequence file [IGVFFI2279YOXY](/sequence-files/IGVFFI2279YOXY/) 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/IGVFDS3774FYIW/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3774FYIW](/auxiliary-sets/IGVFDS3774FYIW/) has a sequence file [IGVFFI2499JLDM](/sequence-files/IGVFFI2499JLDM/) 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/IGVFDS3774FYIW/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8751LXWJ](/measurement-sets/IGVFDS8751LXWJ/) has sequence file(s): [IGVFFI5136JRRS](/sequence-files/IGVFFI5136JRRS/), [IGVFFI6448EYTM](/sequence-files/IGVFFI6448EYTM/), [IGVFFI7706IKZV](/sequence-files/IGVFFI7706IKZV/), [IGVFFI0783JHHG](/sequence-files/IGVFFI0783JHHG/) 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/IGVFDS8751LXWJ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3919NBFE](/auxiliary-sets/IGVFDS3919NBFE/) has sequence file(s): [IGVFFI5800QJKD](/sequence-files/IGVFFI5800QJKD/), [IGVFFI7530AEJH](/sequence-files/IGVFFI7530AEJH/), [IGVFFI5201BBTZ](/sequence-files/IGVFFI5201BBTZ/), [IGVFFI5561SSLS](/sequence-files/IGVFFI5561SSLS/) 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/IGVFDS3919NBFE/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3774FYIW](/auxiliary-sets/IGVFDS3774FYIW/) has sequence file(s): [IGVFFI5934NNRV](/sequence-files/IGVFFI5934NNRV/), [IGVFFI5709SYEW](/sequence-files/IGVFFI5709SYEW/), [IGVFFI2279YOXY](/sequence-files/IGVFFI2279YOXY/), [IGVFFI2499JLDM](/sequence-files/IGVFFI2499JLDM/) 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/IGVFDS3774FYIW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3919NBFE/",
"accession": "IGVFDS3919NBFE",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_sgRNA_LW433"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3774FYIW/",
"accession": "IGVFDS3774FYIW",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_HTO_LW433"
],
"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": "2024-08-16T20:32:07.287429+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/IGVFFI5136JRRS/",
"accession": "IGVFFI5136JRRS",
"aliases": [
"gary-hon:LW433_5_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:18:39.545358+00:00",
"file_format": "fastq",
"file_size": 3004153279,
"href": "/sequence-files/IGVFFI5136JRRS/@@download/IGVFFI5136JRRS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/312e5e2d-802b-42d1-8e46-1a3f3a16cea0/IGVFFI5136JRRS.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//LW433_S2_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6448EYTM/",
"accession": "IGVFFI6448EYTM",
"aliases": [
"gary-hon:LW433_5_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:19:18.938519+00:00",
"file_format": "fastq",
"file_size": 3020512833,
"href": "/sequence-files/IGVFFI6448EYTM/@@download/IGVFFI6448EYTM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/1f2e0e82-0dd3-4954-af1f-69e24fdacdaf/IGVFFI6448EYTM.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//LW433_S2_L005_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7706IKZV/",
"accession": "IGVFFI7706IKZV",
"aliases": [
"gary-hon:LW433_5_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:25:49.285823+00:00",
"file_format": "fastq",
"file_size": 39383802181,
"href": "/sequence-files/IGVFFI7706IKZV/@@download/IGVFFI7706IKZV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/c07a20e5-780a-40b9-bc57-754812f4c0ec/IGVFFI7706IKZV.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//LW433_S2_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0783JHHG/",
"accession": "IGVFFI0783JHHG",
"aliases": [
"gary-hon:LW433_5_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:19:55.333470+00:00",
"file_format": "fastq",
"file_size": 39409259674,
"href": "/sequence-files/IGVFFI0783JHHG/@@download/IGVFFI0783JHHG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/5aec9250-18a9-4944-b5aa-99475a76f5dc/IGVFFI0783JHHG.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//LW433_S2_L005_R1_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/IGVFSM1513DHGW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1513DHGW",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_PB9_LW433"
],
"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_LW433), 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": "2024-11-13T18:51:01.357866+00:00",
"submitter_comment": "Transcriptiome for LW433",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "ccc02008-33ed-410c-985c-093695bc06e6"
}