{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7288IQLC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7288IQLC",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_LW434"
],
"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 [IGVFDS0785CQUX](/auxiliary-sets/IGVFDS0785CQUX/) has a sequence file [IGVFFI3243SSXC](/sequence-files/IGVFFI3243SSXC/) 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/IGVFDS0785CQUX/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS0785CQUX](/auxiliary-sets/IGVFDS0785CQUX/) has a sequence file [IGVFFI3793AHRP](/sequence-files/IGVFFI3793AHRP/) 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/IGVFDS0785CQUX/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS0785CQUX](/auxiliary-sets/IGVFDS0785CQUX/) has a sequence file [IGVFFI9194KPEL](/sequence-files/IGVFFI9194KPEL/) 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/IGVFDS0785CQUX/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS0785CQUX](/auxiliary-sets/IGVFDS0785CQUX/) has a sequence file [IGVFFI2714CFIH](/sequence-files/IGVFFI2714CFIH/) 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/IGVFDS0785CQUX/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS1340IBKW](/auxiliary-sets/IGVFDS1340IBKW/) has a sequence file [IGVFFI3780WHTV](/sequence-files/IGVFFI3780WHTV/) 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/IGVFDS1340IBKW/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS1340IBKW](/auxiliary-sets/IGVFDS1340IBKW/) has a sequence file [IGVFFI2537MGAU](/sequence-files/IGVFFI2537MGAU/) 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/IGVFDS1340IBKW/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS1340IBKW](/auxiliary-sets/IGVFDS1340IBKW/) has a sequence file [IGVFFI0210CMIS](/sequence-files/IGVFFI0210CMIS/) 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/IGVFDS1340IBKW/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS1340IBKW](/auxiliary-sets/IGVFDS1340IBKW/) has a sequence file [IGVFFI3021FRGV](/sequence-files/IGVFFI3021FRGV/) 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/IGVFDS1340IBKW/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0785CQUX](/auxiliary-sets/IGVFDS0785CQUX/) has sequence file(s): [IGVFFI3243SSXC](/sequence-files/IGVFFI3243SSXC/), [IGVFFI3793AHRP](/sequence-files/IGVFFI3793AHRP/), [IGVFFI9194KPEL](/sequence-files/IGVFFI9194KPEL/), [IGVFFI2714CFIH](/sequence-files/IGVFFI2714CFIH/) 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/IGVFDS0785CQUX/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1340IBKW](/auxiliary-sets/IGVFDS1340IBKW/) has sequence file(s): [IGVFFI3780WHTV](/sequence-files/IGVFFI3780WHTV/), [IGVFFI2537MGAU](/sequence-files/IGVFFI2537MGAU/), [IGVFFI0210CMIS](/sequence-files/IGVFFI0210CMIS/), [IGVFFI3021FRGV](/sequence-files/IGVFFI3021FRGV/) 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/IGVFDS1340IBKW/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7288IQLC](/measurement-sets/IGVFDS7288IQLC/) has sequence file(s): [IGVFFI9522WYAF](/sequence-files/IGVFFI9522WYAF/), [IGVFFI7317RZBL](/sequence-files/IGVFFI7317RZBL/), [IGVFFI8012VJJP](/sequence-files/IGVFFI8012VJJP/), [IGVFFI9963MDCI](/sequence-files/IGVFFI9963MDCI/) 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/IGVFDS7288IQLC/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0785CQUX/",
"accession": "IGVFDS0785CQUX",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_sgRNA_LW434"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS1340IBKW/",
"accession": "IGVFDS1340IBKW",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_HTO_LW434"
],
"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": "2024-08-16T20:32:08.861763+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/IGVFFI9522WYAF/",
"accession": "IGVFFI9522WYAF",
"aliases": [
"gary-hon:LW434_5_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:31:40.803790+00:00",
"file_format": "fastq",
"file_size": 2852999101,
"href": "/sequence-files/IGVFFI9522WYAF/@@download/IGVFFI9522WYAF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/2f4b3509-42d2-48a3-bd50-126f7ddf7856/IGVFFI9522WYAF.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//LW434_S3_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7317RZBL/",
"accession": "IGVFFI7317RZBL",
"aliases": [
"gary-hon:LW434_5_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:32:48.175529+00:00",
"file_format": "fastq",
"file_size": 34147491887,
"href": "/sequence-files/IGVFFI7317RZBL/@@download/IGVFFI7317RZBL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/2010c965-94df-4bee-a33e-5ee6e102b9be/IGVFFI7317RZBL.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//LW434_S3_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8012VJJP/",
"accession": "IGVFFI8012VJJP",
"aliases": [
"gary-hon:LW434_5_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:32:14.609155+00:00",
"file_format": "fastq",
"file_size": 2886626352,
"href": "/sequence-files/IGVFFI8012VJJP/@@download/IGVFFI8012VJJP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/418805ea-8209-4828-b11f-9b570335095d/IGVFFI8012VJJP.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//LW434_S3_L005_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9963MDCI/",
"accession": "IGVFFI9963MDCI",
"aliases": [
"gary-hon:LW434_5_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:37:54.887388+00:00",
"file_format": "fastq",
"file_size": 34353954478,
"href": "/sequence-files/IGVFFI9963MDCI/@@download/IGVFFI9963MDCI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/6e0d5379-6abe-41f3-80c4-2ea8ea119826/IGVFFI9963MDCI.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//LW434_S3_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/IGVFSM8133YEXK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8133YEXK",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_PB9_LW434"
],
"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_LW434), 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": "2024-11-13T18:53:24.348008+00:00",
"submitter_comment": "Transcriptiome for LW434",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "f35c3dcd-4cb1-4ace-b641-2bcbaede0b07"
}