{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8110KLML/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8110KLML",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_LW424"
],
"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 [IGVFDS7849GKLL](/auxiliary-sets/IGVFDS7849GKLL/) has a sequence file [IGVFFI8952AWPF](/sequence-files/IGVFFI8952AWPF/) 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/IGVFDS7849GKLL/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS7849GKLL](/auxiliary-sets/IGVFDS7849GKLL/) has a sequence file [IGVFFI0550YHLA](/sequence-files/IGVFFI0550YHLA/) 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/IGVFDS7849GKLL/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS7849GKLL](/auxiliary-sets/IGVFDS7849GKLL/) has a sequence file [IGVFFI4407QPXA](/sequence-files/IGVFFI4407QPXA/) 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/IGVFDS7849GKLL/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS7849GKLL](/auxiliary-sets/IGVFDS7849GKLL/) has a sequence file [IGVFFI2250RJUE](/sequence-files/IGVFFI2250RJUE/) 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/IGVFDS7849GKLL/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3659SZDC](/auxiliary-sets/IGVFDS3659SZDC/) has a sequence file [IGVFFI3444OMRD](/sequence-files/IGVFFI3444OMRD/) 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/IGVFDS3659SZDC/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3659SZDC](/auxiliary-sets/IGVFDS3659SZDC/) has a sequence file [IGVFFI3811FKOC](/sequence-files/IGVFFI3811FKOC/) 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/IGVFDS3659SZDC/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3659SZDC](/auxiliary-sets/IGVFDS3659SZDC/) has a sequence file [IGVFFI2809JKMT](/sequence-files/IGVFFI2809JKMT/) 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/IGVFDS3659SZDC/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS3659SZDC](/auxiliary-sets/IGVFDS3659SZDC/) has a sequence file [IGVFFI2105PSHE](/sequence-files/IGVFFI2105PSHE/) 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/IGVFDS3659SZDC/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7849GKLL](/auxiliary-sets/IGVFDS7849GKLL/) has sequence file(s): [IGVFFI8952AWPF](/sequence-files/IGVFFI8952AWPF/), [IGVFFI0550YHLA](/sequence-files/IGVFFI0550YHLA/), [IGVFFI4407QPXA](/sequence-files/IGVFFI4407QPXA/), [IGVFFI2250RJUE](/sequence-files/IGVFFI2250RJUE/) 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/IGVFDS7849GKLL/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3659SZDC](/auxiliary-sets/IGVFDS3659SZDC/) has sequence file(s): [IGVFFI3444OMRD](/sequence-files/IGVFFI3444OMRD/), [IGVFFI3811FKOC](/sequence-files/IGVFFI3811FKOC/), [IGVFFI2809JKMT](/sequence-files/IGVFFI2809JKMT/), [IGVFFI2105PSHE](/sequence-files/IGVFFI2105PSHE/) 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/IGVFDS3659SZDC/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8110KLML](/measurement-sets/IGVFDS8110KLML/) has sequence file(s): [IGVFFI1835ZYQJ](/sequence-files/IGVFFI1835ZYQJ/), [IGVFFI1876MOKD](/sequence-files/IGVFFI1876MOKD/), [IGVFFI0952BGMF](/sequence-files/IGVFFI0952BGMF/), [IGVFFI6632FFZB](/sequence-files/IGVFFI6632FFZB/) 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/IGVFDS8110KLML/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3659SZDC/",
"accession": "IGVFDS3659SZDC",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_sgRNA_LW424"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7849GKLL/",
"accession": "IGVFDS7849GKLL",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_HTO_LW424"
],
"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": "2024-08-16T20:31:50.263781+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/IGVFFI1835ZYQJ/",
"accession": "IGVFFI1835ZYQJ",
"aliases": [
"gary-hon:LW424_4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:28:13.180876+00:00",
"file_format": "fastq",
"file_size": 2303338467,
"href": "/sequence-files/IGVFFI1835ZYQJ/@@download/IGVFFI1835ZYQJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/bff0dbbc-6e6c-4c23-9669-72c4767f48a1/IGVFFI1835ZYQJ.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//LW424_S2_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1876MOKD/",
"accession": "IGVFFI1876MOKD",
"aliases": [
"gary-hon:LW424_4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:29:16.444058+00:00",
"file_format": "fastq",
"file_size": 27307857935,
"href": "/sequence-files/IGVFFI1876MOKD/@@download/IGVFFI1876MOKD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/2d0c1887-ede6-48f8-b682-ce4a9fb7ff4b/IGVFFI1876MOKD.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//LW424_S2_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0952BGMF/",
"accession": "IGVFFI0952BGMF",
"aliases": [
"gary-hon:LW424_4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:28:43.203234+00:00",
"file_format": "fastq",
"file_size": 2636479741,
"href": "/sequence-files/IGVFFI0952BGMF/@@download/IGVFFI0952BGMF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/2bb7db40-e790-4576-ab69-90ed1ba4b323/IGVFFI0952BGMF.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//LW424_S2_L004_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6632FFZB/",
"accession": "IGVFFI6632FFZB",
"aliases": [
"gary-hon:LW424_4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:33:19.039925+00:00",
"file_format": "fastq",
"file_size": 27590644970,
"href": "/sequence-files/IGVFFI6632FFZB/@@download/IGVFFI6632FFZB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/3222edbb-f017-47ff-ad4b-8e74cd457f7b/IGVFFI6632FFZB.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//LW424_S2_L004_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/IGVFSM3002CFHI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3002CFHI",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_Inducible_LW424"
],
"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_LW424), 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": "2024-11-13T21:01:26.842204+00:00",
"submitter_comment": "Transcriptiome for LW424",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "c0462885-be6a-4eeb-903b-ffef714c4035"
}