{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1334EIHS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1334EIHS",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW231"
],
"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": "Measurement set [IGVFDS1334EIHS](/measurement-sets/IGVFDS1334EIHS/) has sequence file(s) [IGVFFI2743LEOZ](/sequence-files/IGVFFI2743LEOZ/), [IGVFFI7895WVYF](/sequence-files/IGVFFI7895WVYF/), [IGVFFI8033LYZK](/sequence-files/IGVFFI8033LYZK/), [IGVFFI2558ARIF](/sequence-files/IGVFFI2558ARIF/) 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/IGVFDS1334EIHS/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1334EIHS](/measurement-sets/IGVFDS1334EIHS/) has sequence file(s): [IGVFFI2743LEOZ](/sequence-files/IGVFFI2743LEOZ/), [IGVFFI7895WVYF](/sequence-files/IGVFFI7895WVYF/), [IGVFFI8033LYZK](/sequence-files/IGVFFI8033LYZK/), [IGVFFI2558ARIF](/sequence-files/IGVFFI2558ARIF/) 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/IGVFDS1334EIHS/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7504HTXW](/auxiliary-sets/IGVFDS7504HTXW/) has sequence file(s) [IGVFFI3844RZSE](/sequence-files/IGVFFI3844RZSE/), [IGVFFI7424BNYL](/sequence-files/IGVFFI7424BNYL/), [IGVFFI0084HLJI](/sequence-files/IGVFFI0084HLJI/), [IGVFFI2134DIIO](/sequence-files/IGVFFI2134DIIO/), [IGVFFI5003ILCS](/sequence-files/IGVFFI5003ILCS/), [IGVFFI9965OPJT](/sequence-files/IGVFFI9965OPJT/), [IGVFFI9656IWUX](/sequence-files/IGVFFI9656IWUX/), [IGVFFI2044LHZP](/sequence-files/IGVFFI2044LHZP/) 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/IGVFDS7504HTXW/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7504HTXW](/auxiliary-sets/IGVFDS7504HTXW/) has sequence file(s): [IGVFFI3844RZSE](/sequence-files/IGVFFI3844RZSE/), [IGVFFI7424BNYL](/sequence-files/IGVFFI7424BNYL/), [IGVFFI0084HLJI](/sequence-files/IGVFFI0084HLJI/), [IGVFFI2134DIIO](/sequence-files/IGVFFI2134DIIO/), [IGVFFI5003ILCS](/sequence-files/IGVFFI5003ILCS/), [IGVFFI9965OPJT](/sequence-files/IGVFFI9965OPJT/), [IGVFFI9656IWUX](/sequence-files/IGVFFI9656IWUX/), [IGVFFI2044LHZP](/sequence-files/IGVFFI2044LHZP/) 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/IGVFDS7504HTXW/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5986XHYV](/auxiliary-sets/IGVFDS5986XHYV/) has sequence file(s) [IGVFFI1563TIUE](/sequence-files/IGVFFI1563TIUE/), [IGVFFI4146MFBE](/sequence-files/IGVFFI4146MFBE/), [IGVFFI4745WZDI](/sequence-files/IGVFFI4745WZDI/), [IGVFFI0503LCOS](/sequence-files/IGVFFI0503LCOS/), [IGVFFI8165EFZM](/sequence-files/IGVFFI8165EFZM/), [IGVFFI2505NLLH](/sequence-files/IGVFFI2505NLLH/), [IGVFFI5897DBBP](/sequence-files/IGVFFI5897DBBP/), [IGVFFI3760ZTYQ](/sequence-files/IGVFFI3760ZTYQ/) 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/IGVFDS5986XHYV/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5986XHYV](/auxiliary-sets/IGVFDS5986XHYV/) has sequence file(s): [IGVFFI1563TIUE](/sequence-files/IGVFFI1563TIUE/), [IGVFFI4146MFBE](/sequence-files/IGVFFI4146MFBE/), [IGVFFI4745WZDI](/sequence-files/IGVFFI4745WZDI/), [IGVFFI0503LCOS](/sequence-files/IGVFFI0503LCOS/), [IGVFFI8165EFZM](/sequence-files/IGVFFI8165EFZM/), [IGVFFI2505NLLH](/sequence-files/IGVFFI2505NLLH/), [IGVFFI5897DBBP](/sequence-files/IGVFFI5897DBBP/), [IGVFFI3760ZTYQ](/sequence-files/IGVFFI3760ZTYQ/) 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/IGVFDS5986XHYV/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5986XHYV/",
"accession": "IGVFDS5986XHYV",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW231"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7504HTXW/",
"accession": "IGVFDS7504HTXW",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW231"
],
"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": "2024-02-15T23:43:11.453254+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/IGVFFI2743LEOZ/",
"accession": "IGVFFI2743LEOZ",
"aliases": [
"gary-hon:LW231_4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T19:54:47.314982+00:00",
"file_format": "fastq",
"file_size": 1806532916,
"href": "/sequence-files/IGVFFI2743LEOZ/@@download/IGVFFI2743LEOZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/b2080f28-179e-44f6-af1f-e6da7f91ee79/IGVFFI2743LEOZ.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/LW231_S3_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7895WVYF/",
"accession": "IGVFFI7895WVYF",
"aliases": [
"gary-hon:LW231_4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T19:58:33.733979+00:00",
"file_format": "fastq",
"file_size": 20620445191,
"href": "/sequence-files/IGVFFI7895WVYF/@@download/IGVFFI7895WVYF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/1c148f26-66b2-439f-accd-3b919183d7dd/IGVFFI7895WVYF.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/LW231_S3_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8033LYZK/",
"accession": "IGVFFI8033LYZK",
"aliases": [
"gary-hon:LW231_4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T19:55:08.721689+00:00",
"file_format": "fastq",
"file_size": 1842034078,
"href": "/sequence-files/IGVFFI8033LYZK/@@download/IGVFFI8033LYZK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/3f9b2b4e-7317-4a1f-a3de-70586f3d8c66/IGVFFI8033LYZK.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/LW231_S3_L004_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2558ARIF/",
"accession": "IGVFFI2558ARIF",
"aliases": [
"gary-hon:LW231_4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T19:55:30.159293+00:00",
"file_format": "fastq",
"file_size": 20839306981,
"href": "/sequence-files/IGVFFI2558ARIF/@@download/IGVFFI2558ARIF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/6e61aef3-a5aa-4352-a7cb-645e5fc6adbf/IGVFFI2558ARIF.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/LW231_S3_L004_R1_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/IGVFSM7740VKXC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7740VKXC",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW231"
],
"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_LW261), 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": "2024-02-21T18:17:06.347576+00:00",
"submitter_comment": "Transcriptiome for LW231'",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "498f2f67-cbce-447d-a51a-60bd5a21fc9e"
}