{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8701ERXN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8701ERXN",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW238"
],
"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 [IGVFDS6402AFPQ](/auxiliary-sets/IGVFDS6402AFPQ/) has sequence file(s) [IGVFFI7732YRYL](/sequence-files/IGVFFI7732YRYL/), [IGVFFI3342AZOL](/sequence-files/IGVFFI3342AZOL/), [IGVFFI2001BUVU](/sequence-files/IGVFFI2001BUVU/), [IGVFFI2156WUHQ](/sequence-files/IGVFFI2156WUHQ/), [IGVFFI2591CCVN](/sequence-files/IGVFFI2591CCVN/), [IGVFFI8893RYFI](/sequence-files/IGVFFI8893RYFI/), [IGVFFI1306YVIM](/sequence-files/IGVFFI1306YVIM/), [IGVFFI0841DIBZ](/sequence-files/IGVFFI0841DIBZ/) 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/IGVFDS6402AFPQ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6402AFPQ](/auxiliary-sets/IGVFDS6402AFPQ/) has sequence file(s): [IGVFFI7732YRYL](/sequence-files/IGVFFI7732YRYL/), [IGVFFI3342AZOL](/sequence-files/IGVFFI3342AZOL/), [IGVFFI2001BUVU](/sequence-files/IGVFFI2001BUVU/), [IGVFFI2156WUHQ](/sequence-files/IGVFFI2156WUHQ/), [IGVFFI2591CCVN](/sequence-files/IGVFFI2591CCVN/), [IGVFFI8893RYFI](/sequence-files/IGVFFI8893RYFI/), [IGVFFI1306YVIM](/sequence-files/IGVFFI1306YVIM/), [IGVFFI0841DIBZ](/sequence-files/IGVFFI0841DIBZ/) 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/IGVFDS6402AFPQ/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7019VPKV](/auxiliary-sets/IGVFDS7019VPKV/) has sequence file(s) [IGVFFI5790IQTB](/sequence-files/IGVFFI5790IQTB/), [IGVFFI0279NKCJ](/sequence-files/IGVFFI0279NKCJ/), [IGVFFI8978ELVT](/sequence-files/IGVFFI8978ELVT/), [IGVFFI7459ZLGX](/sequence-files/IGVFFI7459ZLGX/), [IGVFFI3499NNMI](/sequence-files/IGVFFI3499NNMI/), [IGVFFI1992QYNR](/sequence-files/IGVFFI1992QYNR/), [IGVFFI6560RTAA](/sequence-files/IGVFFI6560RTAA/), [IGVFFI8362NKUV](/sequence-files/IGVFFI8362NKUV/) 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/IGVFDS7019VPKV/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7019VPKV](/auxiliary-sets/IGVFDS7019VPKV/) has sequence file(s): [IGVFFI5790IQTB](/sequence-files/IGVFFI5790IQTB/), [IGVFFI0279NKCJ](/sequence-files/IGVFFI0279NKCJ/), [IGVFFI8978ELVT](/sequence-files/IGVFFI8978ELVT/), [IGVFFI7459ZLGX](/sequence-files/IGVFFI7459ZLGX/), [IGVFFI3499NNMI](/sequence-files/IGVFFI3499NNMI/), [IGVFFI1992QYNR](/sequence-files/IGVFFI1992QYNR/), [IGVFFI6560RTAA](/sequence-files/IGVFFI6560RTAA/), [IGVFFI8362NKUV](/sequence-files/IGVFFI8362NKUV/) 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/IGVFDS7019VPKV/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8701ERXN](/measurement-sets/IGVFDS8701ERXN/) has sequence file(s) [IGVFFI3564JWVE](/sequence-files/IGVFFI3564JWVE/), [IGVFFI6072HGKG](/sequence-files/IGVFFI6072HGKG/), [IGVFFI1665WXLP](/sequence-files/IGVFFI1665WXLP/), [IGVFFI5480FCPQ](/sequence-files/IGVFFI5480FCPQ/) 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/IGVFDS8701ERXN/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8701ERXN](/measurement-sets/IGVFDS8701ERXN/) has sequence file(s): [IGVFFI3564JWVE](/sequence-files/IGVFFI3564JWVE/), [IGVFFI6072HGKG](/sequence-files/IGVFFI6072HGKG/), [IGVFFI1665WXLP](/sequence-files/IGVFFI1665WXLP/), [IGVFFI5480FCPQ](/sequence-files/IGVFFI5480FCPQ/) 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/IGVFDS8701ERXN/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6402AFPQ/",
"accession": "IGVFDS6402AFPQ",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW238"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7019VPKV/",
"accession": "IGVFDS7019VPKV",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW238"
],
"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": "2024-02-15T23:43:19.627573+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/IGVFFI3564JWVE/",
"accession": "IGVFFI3564JWVE",
"aliases": [
"gary-hon:LW238_4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:49:52.800908+00:00",
"file_format": "fastq",
"file_size": 1455951455,
"href": "/sequence-files/IGVFFI3564JWVE/@@download/IGVFFI3564JWVE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/9cbd1e51-8829-43f9-af21-b8d99e6fd1f8/IGVFFI3564JWVE.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/LW238_S10_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6072HGKG/",
"accession": "IGVFFI6072HGKG",
"aliases": [
"gary-hon:LW238_4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:53:07.051126+00:00",
"file_format": "fastq",
"file_size": 17167523226,
"href": "/sequence-files/IGVFFI6072HGKG/@@download/IGVFFI6072HGKG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/6ed9d451-dad9-4a4b-a193-9f4b68b72aed/IGVFFI6072HGKG.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/LW238_S10_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1665WXLP/",
"accession": "IGVFFI1665WXLP",
"aliases": [
"gary-hon:LW238_4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:50:29.018099+00:00",
"file_format": "fastq",
"file_size": 17556802014,
"href": "/sequence-files/IGVFFI1665WXLP/@@download/IGVFFI1665WXLP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/8adbe5dd-052b-4bbe-b69f-1f1ed947769a/IGVFFI1665WXLP.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/LW238_S10_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5480FCPQ/",
"accession": "IGVFFI5480FCPQ",
"aliases": [
"gary-hon:LW238_4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:50:10.751983+00:00",
"file_format": "fastq",
"file_size": 1479704236,
"href": "/sequence-files/IGVFFI5480FCPQ/@@download/IGVFFI5480FCPQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/718b3570-1802-41d7-8b99-d3657cc83803/IGVFFI5480FCPQ.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/LW238_S10_L004_I2_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/IGVFSM9326DRHX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9326DRHX",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW238"
],
"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_LW268), 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": "2024-02-21T18:34:11.442738+00:00",
"submitter_comment": "Transcriptiome for LW238'",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "317a2967-f86a-4a61-834e-4143f4d619d2"
}