{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2593KURF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2593KURF",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW237"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003660/",
"status": "released",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3212YIVB](/auxiliary-sets/IGVFDS3212YIVB/) has sequence file(s) [IGVFFI9859AZBM](/sequence-files/IGVFFI9859AZBM/), [IGVFFI8394REEI](/sequence-files/IGVFFI8394REEI/), [IGVFFI5714GMWE](/sequence-files/IGVFFI5714GMWE/), [IGVFFI9059QESJ](/sequence-files/IGVFFI9059QESJ/), [IGVFFI8864XBJJ](/sequence-files/IGVFFI8864XBJJ/), [IGVFFI6690RGJL](/sequence-files/IGVFFI6690RGJL/), [IGVFFI1258HMIV](/sequence-files/IGVFFI1258HMIV/), [IGVFFI1304WFWQ](/sequence-files/IGVFFI1304WFWQ/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS3212YIVB/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3212YIVB](/auxiliary-sets/IGVFDS3212YIVB/) has sequence file(s): [IGVFFI9859AZBM](/sequence-files/IGVFFI9859AZBM/), [IGVFFI8394REEI](/sequence-files/IGVFFI8394REEI/), [IGVFFI5714GMWE](/sequence-files/IGVFFI5714GMWE/), [IGVFFI9059QESJ](/sequence-files/IGVFFI9059QESJ/), [IGVFFI8864XBJJ](/sequence-files/IGVFFI8864XBJJ/), [IGVFFI6690RGJL](/sequence-files/IGVFFI6690RGJL/), [IGVFFI1258HMIV](/sequence-files/IGVFFI1258HMIV/), [IGVFFI1304WFWQ](/sequence-files/IGVFFI1304WFWQ/) 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/IGVFDS3212YIVB/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2593KURF](/measurement-sets/IGVFDS2593KURF/) has sequence file(s) [IGVFFI6068CGKL](/sequence-files/IGVFFI6068CGKL/), [IGVFFI1833UHUB](/sequence-files/IGVFFI1833UHUB/), [IGVFFI7525DURE](/sequence-files/IGVFFI7525DURE/), [IGVFFI4391DDCO](/sequence-files/IGVFFI4391DDCO/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS2593KURF/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2593KURF](/measurement-sets/IGVFDS2593KURF/) has sequence file(s): [IGVFFI6068CGKL](/sequence-files/IGVFFI6068CGKL/), [IGVFFI1833UHUB](/sequence-files/IGVFFI1833UHUB/), [IGVFFI7525DURE](/sequence-files/IGVFFI7525DURE/), [IGVFFI4391DDCO](/sequence-files/IGVFFI4391DDCO/) 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/IGVFDS2593KURF/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2406OSFC](/auxiliary-sets/IGVFDS2406OSFC/) has sequence file(s) [IGVFFI4271ZYNK](/sequence-files/IGVFFI4271ZYNK/), [IGVFFI4753ESNB](/sequence-files/IGVFFI4753ESNB/), [IGVFFI7543WDMT](/sequence-files/IGVFFI7543WDMT/), [IGVFFI6111FHSJ](/sequence-files/IGVFFI6111FHSJ/), [IGVFFI0561MNSA](/sequence-files/IGVFFI0561MNSA/), [IGVFFI9370EAFR](/sequence-files/IGVFFI9370EAFR/), [IGVFFI7058PKFB](/sequence-files/IGVFFI7058PKFB/), [IGVFFI3224UVDH](/sequence-files/IGVFFI3224UVDH/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS2406OSFC/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2406OSFC](/auxiliary-sets/IGVFDS2406OSFC/) has sequence file(s): [IGVFFI4271ZYNK](/sequence-files/IGVFFI4271ZYNK/), [IGVFFI4753ESNB](/sequence-files/IGVFFI4753ESNB/), [IGVFFI7543WDMT](/sequence-files/IGVFFI7543WDMT/), [IGVFFI6111FHSJ](/sequence-files/IGVFFI6111FHSJ/), [IGVFFI0561MNSA](/sequence-files/IGVFFI0561MNSA/), [IGVFFI9370EAFR](/sequence-files/IGVFFI9370EAFR/), [IGVFFI7058PKFB](/sequence-files/IGVFFI7058PKFB/), [IGVFFI3224UVDH](/sequence-files/IGVFFI3224UVDH/) 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/IGVFDS2406OSFC/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2406OSFC/",
"accession": "IGVFDS2406OSFC",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW237"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3212YIVB/",
"accession": "IGVFDS3212YIVB",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW237"
],
"file_set_type": "gRNA 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": "2024-02-15T23:43:18.784377+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI6068CGKL/",
"accession": "IGVFFI6068CGKL",
"aliases": [
"gary-hon:LW237_4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:41:02.904020+00:00",
"file_format": "fastq",
"file_size": 2112964722,
"href": "/sequence-files/IGVFFI6068CGKL/@@download/IGVFFI6068CGKL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/83f2587d-3a58-41a7-bf96-36e01f3214cc/IGVFFI6068CGKL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-22-McDermott-NovaSeq.10X/10X/LW237_S9_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1833UHUB/",
"accession": "IGVFFI1833UHUB",
"aliases": [
"gary-hon:LW237_4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:41:26.489409+00:00",
"file_format": "fastq",
"file_size": 2057012078,
"href": "/sequence-files/IGVFFI1833UHUB/@@download/IGVFFI1833UHUB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/21c6aba1-47b5-45b1-ac37-b492ae8fe680/IGVFFI1833UHUB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-22-McDermott-NovaSeq.10X/10X/LW237_S9_L004_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7525DURE/",
"accession": "IGVFFI7525DURE",
"aliases": [
"gary-hon:LW237_4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:41:49.275002+00:00",
"file_format": "fastq",
"file_size": 27892625311,
"href": "/sequence-files/IGVFFI7525DURE/@@download/IGVFFI7525DURE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/48cd130d-11d5-4544-a584-cf0ab21a0192/IGVFFI7525DURE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-22-McDermott-NovaSeq.10X/10X/LW237_S9_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4391DDCO/",
"accession": "IGVFFI4391DDCO",
"aliases": [
"gary-hon:LW237_4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:45:52.011170+00:00",
"file_format": "fastq",
"file_size": 27513053316,
"href": "/sequence-files/IGVFFI4391DDCO/@@download/IGVFFI4391DDCO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/f8232083-9cb2-4ae1-84f0-5ec5dc696611/IGVFFI4391DDCO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-22-McDermott-NovaSeq.10X/10X/LW237_S9_L004_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9192YMGI/"
],
"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/IGVFSM2329UXLZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2329UXLZ",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW237"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS9629YZLO/",
"accession": "IGVFDS9629YZLO",
"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_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW267), male, 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": "2024-02-21T18:31:32.085712+00:00",
"submitter_comment": "Transcriptiome for LW237'",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "c26b6951-d9c1-4585-8831-d3168a1427c2"
}