{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3847PDAQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3847PDAQ",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_LW423"
],
"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 [IGVFDS8811SXIK](/auxiliary-sets/IGVFDS8811SXIK/) has a sequence file [IGVFFI4555ANDX](/sequence-files/IGVFFI4555ANDX/) 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/IGVFDS8811SXIK/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS8811SXIK](/auxiliary-sets/IGVFDS8811SXIK/) has a sequence file [IGVFFI6443EILQ](/sequence-files/IGVFFI6443EILQ/) 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/IGVFDS8811SXIK/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS8811SXIK](/auxiliary-sets/IGVFDS8811SXIK/) has a sequence file [IGVFFI3109VYPD](/sequence-files/IGVFFI3109VYPD/) 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/IGVFDS8811SXIK/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS8811SXIK](/auxiliary-sets/IGVFDS8811SXIK/) has a sequence file [IGVFFI0997EUGR](/sequence-files/IGVFFI0997EUGR/) 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/IGVFDS8811SXIK/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS9735REPA](/auxiliary-sets/IGVFDS9735REPA/) has a sequence file [IGVFFI1024SNXF](/sequence-files/IGVFFI1024SNXF/) 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/IGVFDS9735REPA/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS9735REPA](/auxiliary-sets/IGVFDS9735REPA/) has a sequence file [IGVFFI8917IMMW](/sequence-files/IGVFFI8917IMMW/) 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/IGVFDS9735REPA/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS9735REPA](/auxiliary-sets/IGVFDS9735REPA/) has a sequence file [IGVFFI1900TGMR](/sequence-files/IGVFFI1900TGMR/) 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/IGVFDS9735REPA/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS9735REPA](/auxiliary-sets/IGVFDS9735REPA/) has a sequence file [IGVFFI3207RGMA](/sequence-files/IGVFFI3207RGMA/) 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/IGVFDS9735REPA/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3847PDAQ](/measurement-sets/IGVFDS3847PDAQ/) has sequence file(s): [IGVFFI2982QCIT](/sequence-files/IGVFFI2982QCIT/), [IGVFFI1834YRMT](/sequence-files/IGVFFI1834YRMT/), [IGVFFI3496VXKF](/sequence-files/IGVFFI3496VXKF/), [IGVFFI8812OOXA](/sequence-files/IGVFFI8812OOXA/) 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/IGVFDS3847PDAQ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8811SXIK](/auxiliary-sets/IGVFDS8811SXIK/) has sequence file(s): [IGVFFI4555ANDX](/sequence-files/IGVFFI4555ANDX/), [IGVFFI6443EILQ](/sequence-files/IGVFFI6443EILQ/), [IGVFFI3109VYPD](/sequence-files/IGVFFI3109VYPD/), [IGVFFI0997EUGR](/sequence-files/IGVFFI0997EUGR/) 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/IGVFDS8811SXIK/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9735REPA](/auxiliary-sets/IGVFDS9735REPA/) has sequence file(s): [IGVFFI1024SNXF](/sequence-files/IGVFFI1024SNXF/), [IGVFFI8917IMMW](/sequence-files/IGVFFI8917IMMW/), [IGVFFI1900TGMR](/sequence-files/IGVFFI1900TGMR/), [IGVFFI3207RGMA](/sequence-files/IGVFFI3207RGMA/) 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/IGVFDS9735REPA/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9735REPA/",
"accession": "IGVFDS9735REPA",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_sgRNA_LW423"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS8811SXIK/",
"accession": "IGVFDS8811SXIK",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_Inducible_HTO_LW423"
],
"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": "2024-08-16T20:31:48.107972+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/IGVFFI2982QCIT/",
"accession": "IGVFFI2982QCIT",
"aliases": [
"gary-hon:LW423_4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:18:56.961130+00:00",
"file_format": "fastq",
"file_size": 2279204331,
"href": "/sequence-files/IGVFFI2982QCIT/@@download/IGVFFI2982QCIT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/cebb2fc6-787b-4a0f-8f1f-cca94cfd5dc7/IGVFFI2982QCIT.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//LW423_S1_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1834YRMT/",
"accession": "IGVFFI1834YRMT",
"aliases": [
"gary-hon:LW423_4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:19:54.720988+00:00",
"file_format": "fastq",
"file_size": 27722158109,
"href": "/sequence-files/IGVFFI1834YRMT/@@download/IGVFFI1834YRMT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/0f113eba-3906-4fab-ace5-beeff981aa8c/IGVFFI1834YRMT.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//LW423_S1_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3496VXKF/",
"accession": "IGVFFI3496VXKF",
"aliases": [
"gary-hon:LW423_4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:24:03.935537+00:00",
"file_format": "fastq",
"file_size": 27919487992,
"href": "/sequence-files/IGVFFI3496VXKF/@@download/IGVFFI3496VXKF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/f20f66c1-0505-4a5c-82bc-280d3cc1a81d/IGVFFI3496VXKF.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//LW423_S1_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8812OOXA/",
"accession": "IGVFFI8812OOXA",
"aliases": [
"gary-hon:LW423_4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:19:26.883013+00:00",
"file_format": "fastq",
"file_size": 2078710748,
"href": "/sequence-files/IGVFFI8812OOXA/@@download/IGVFFI8812OOXA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/e49b7550-bb28-41bd-9320-a533630e5961/IGVFFI8812OOXA.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//LW423_S1_L004_I2_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/IGVFSM3015ZQZL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3015ZQZL",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_Inducible_LW423"
],
"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_LW423), 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": "2024-11-13T20:59:31.928020+00:00",
"submitter_comment": "Transcriptiome for LW423",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "e7a9fa68-c881-4e69-ad55-58b14c53322e"
}