{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS0019ZVVN/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0019ZVVN",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW232"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0019ZVVN](/auxiliary-sets/IGVFDS0019ZVVN/) has sequence file(s) [IGVFFI6307ZDPG](/sequence-files/IGVFFI6307ZDPG/), [IGVFFI2739CHPC](/sequence-files/IGVFFI2739CHPC/), [IGVFFI5906NTWL](/sequence-files/IGVFFI5906NTWL/), [IGVFFI9506XCZX](/sequence-files/IGVFFI9506XCZX/), [IGVFFI7493FEQQ](/sequence-files/IGVFFI7493FEQQ/), [IGVFFI7011YGKB](/sequence-files/IGVFFI7011YGKB/), [IGVFFI9497SCBF](/sequence-files/IGVFFI9497SCBF/), [IGVFFI7480GPXJ](/sequence-files/IGVFFI7480GPXJ/) 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/IGVFDS0019ZVVN/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0019ZVVN](/auxiliary-sets/IGVFDS0019ZVVN/) has sequence file(s): [IGVFFI6307ZDPG](/sequence-files/IGVFFI6307ZDPG/), [IGVFFI2739CHPC](/sequence-files/IGVFFI2739CHPC/), [IGVFFI5906NTWL](/sequence-files/IGVFFI5906NTWL/), [IGVFFI9506XCZX](/sequence-files/IGVFFI9506XCZX/), [IGVFFI7493FEQQ](/sequence-files/IGVFFI7493FEQQ/), [IGVFFI7011YGKB](/sequence-files/IGVFFI7011YGKB/), [IGVFFI9497SCBF](/sequence-files/IGVFFI9497SCBF/), [IGVFFI7480GPXJ](/sequence-files/IGVFFI7480GPXJ/) 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/IGVFDS0019ZVVN/"
}
]
},
"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": "2024-02-15T23:35:33.164514+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "cell hashing barcode sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI6307ZDPG/",
"accession": "IGVFFI6307ZDPG",
"aliases": [
"gary-hon:LW232C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:21:02.832157+00:00",
"file_format": "fastq",
"file_size": 142255850,
"href": "/sequence-files/IGVFFI6307ZDPG/@@download/IGVFFI6307ZDPG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/e1377467-8f4d-446e-beef-60e0990322a6/IGVFFI6307ZDPG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW232C_S10_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2739CHPC/",
"accession": "IGVFFI2739CHPC",
"aliases": [
"gary-hon:LW232C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:21:26.540062+00:00",
"file_format": "fastq",
"file_size": 761088795,
"href": "/sequence-files/IGVFFI2739CHPC/@@download/IGVFFI2739CHPC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/27c5cdf4-1cde-4513-a728-2d38291b0d68/IGVFFI2739CHPC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW232C_S10_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5906NTWL/",
"accession": "IGVFFI5906NTWL",
"aliases": [
"gary-hon:LW232C_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:21:37.050025+00:00",
"file_format": "fastq",
"file_size": 130275960,
"href": "/sequence-files/IGVFFI5906NTWL/@@download/IGVFFI5906NTWL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/fd487428-b87d-4cda-864f-d1937769bb30/IGVFFI5906NTWL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW232C_S10_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9506XCZX/",
"accession": "IGVFFI9506XCZX",
"aliases": [
"gary-hon:LW232C_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:21:42.590482+00:00",
"file_format": "fastq",
"file_size": 113232485,
"href": "/sequence-files/IGVFFI9506XCZX/@@download/IGVFFI9506XCZX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/721ad2f2-fad8-4110-81f7-3f0e84e449aa/IGVFFI9506XCZX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW232C_S10_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7493FEQQ/",
"accession": "IGVFFI7493FEQQ",
"aliases": [
"gary-hon:LW232C_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:21:47.619049+00:00",
"file_format": "fastq",
"file_size": 374370780,
"href": "/sequence-files/IGVFFI7493FEQQ/@@download/IGVFFI7493FEQQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/ab14198b-2d19-4ba3-b733-93efe21e1f09/IGVFFI7493FEQQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW232C_S10_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7011YGKB/",
"accession": "IGVFFI7011YGKB",
"aliases": [
"gary-hon:LW232C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:21:13.662340+00:00",
"file_format": "fastq",
"file_size": 121326869,
"href": "/sequence-files/IGVFFI7011YGKB/@@download/IGVFFI7011YGKB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/a4defa14-6e20-4e32-a20d-1645d8ba1b05/IGVFFI7011YGKB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW232C_S10_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9497SCBF/",
"accession": "IGVFFI9497SCBF",
"aliases": [
"gary-hon:LW232C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:21:19.130101+00:00",
"file_format": "fastq",
"file_size": 402995098,
"href": "/sequence-files/IGVFFI9497SCBF/@@download/IGVFFI9497SCBF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/f69bbfa4-fdce-4c3d-b96c-24e1c5444c53/IGVFFI9497SCBF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW232C_S10_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7480GPXJ/",
"accession": "IGVFFI7480GPXJ",
"aliases": [
"gary-hon:LW232C_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:21:54.817399+00:00",
"file_format": "fastq",
"file_size": 702753933,
"href": "/sequence-files/IGVFFI7480GPXJ/@@download/IGVFFI7480GPXJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/42f5d667-640b-4b50-b09f-5ce9f5812915/IGVFFI7480GPXJ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW232C_S10_L002_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9192YMGI/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS9005AVSB/",
"accession": "IGVFDS9005AVSB",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW232"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"notes": "File_set_type enum cell hashing has been renamed to be cell hashing barcode sequencing.",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4953FLXN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4953FLXN",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW232"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"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_LW262), 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": "12",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-02-21T18:21:02.832157+00:00",
"summary": "cell hashing barcode sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "79e5bf3f-8706-4f62-b63e-6d072db9a8a8"
}