{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS9856AQIW/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS9856AQIW",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW233"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9856AQIW](/auxiliary-sets/IGVFDS9856AQIW/) has sequence file(s) [IGVFFI5551RHYT](/sequence-files/IGVFFI5551RHYT/), [IGVFFI6398GHSK](/sequence-files/IGVFFI6398GHSK/), [IGVFFI2977AAIK](/sequence-files/IGVFFI2977AAIK/), [IGVFFI0455IRKB](/sequence-files/IGVFFI0455IRKB/), [IGVFFI4423PKGT](/sequence-files/IGVFFI4423PKGT/), [IGVFFI6674LNJC](/sequence-files/IGVFFI6674LNJC/), [IGVFFI2799DOBT](/sequence-files/IGVFFI2799DOBT/), [IGVFFI6392CKYO](/sequence-files/IGVFFI6392CKYO/) 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/IGVFDS9856AQIW/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9856AQIW](/auxiliary-sets/IGVFDS9856AQIW/) has sequence file(s): [IGVFFI5551RHYT](/sequence-files/IGVFFI5551RHYT/), [IGVFFI6398GHSK](/sequence-files/IGVFFI6398GHSK/), [IGVFFI2977AAIK](/sequence-files/IGVFFI2977AAIK/), [IGVFFI0455IRKB](/sequence-files/IGVFFI0455IRKB/), [IGVFFI4423PKGT](/sequence-files/IGVFFI4423PKGT/), [IGVFFI6674LNJC](/sequence-files/IGVFFI6674LNJC/), [IGVFFI2799DOBT](/sequence-files/IGVFFI2799DOBT/), [IGVFFI6392CKYO](/sequence-files/IGVFFI6392CKYO/) 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/IGVFDS9856AQIW/"
}
]
},
"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": "2024-02-15T23:35:35.539167+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/IGVFFI5551RHYT/",
"accession": "IGVFFI5551RHYT",
"aliases": [
"gary-hon:LW233C_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:24:06.444976+00:00",
"file_format": "fastq",
"file_size": 115675627,
"href": "/sequence-files/IGVFFI5551RHYT/@@download/IGVFFI5551RHYT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/c98cbb40-a4aa-4cd4-849c-b3e4cee8328a/IGVFFI5551RHYT.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/LW233C_S11_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6398GHSK/",
"accession": "IGVFFI6398GHSK",
"aliases": [
"gary-hon:LW233C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:23:42.245717+00:00",
"file_format": "fastq",
"file_size": 133568110,
"href": "/sequence-files/IGVFFI6398GHSK/@@download/IGVFFI6398GHSK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/560ec7a2-fa85-49d3-bb03-e84cc9efab6e/IGVFFI6398GHSK.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/LW233C_S11_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2977AAIK/",
"accession": "IGVFFI2977AAIK",
"aliases": [
"gary-hon:LW233C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:23:47.520564+00:00",
"file_format": "fastq",
"file_size": 441550954,
"href": "/sequence-files/IGVFFI2977AAIK/@@download/IGVFFI2977AAIK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/e15fe52c-b213-4b9a-a4b3-f60845981ec8/IGVFFI2977AAIK.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/LW233C_S11_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0455IRKB/",
"accession": "IGVFFI0455IRKB",
"aliases": [
"gary-hon:LW233C_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:24:11.666183+00:00",
"file_format": "fastq",
"file_size": 119488062,
"href": "/sequence-files/IGVFFI0455IRKB/@@download/IGVFFI0455IRKB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/8bc7ce70-53b6-47d5-a142-05adf134e0f1/IGVFFI0455IRKB.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/LW233C_S11_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4423PKGT/",
"accession": "IGVFFI4423PKGT",
"aliases": [
"gary-hon:LW233C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:23:55.252222+00:00",
"file_format": "fastq",
"file_size": 823844916,
"href": "/sequence-files/IGVFFI4423PKGT/@@download/IGVFFI4423PKGT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/33c65970-2eb6-4f94-8e5d-f35c52197728/IGVFFI4423PKGT.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/LW233C_S11_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6674LNJC/",
"accession": "IGVFFI6674LNJC",
"aliases": [
"gary-hon:LW233C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:23:36.330004+00:00",
"file_format": "fastq",
"file_size": 124139032,
"href": "/sequence-files/IGVFFI6674LNJC/@@download/IGVFFI6674LNJC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/43b85134-82a6-4788-896c-109adcb0a7cb/IGVFFI6674LNJC.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/LW233C_S11_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2799DOBT/",
"accession": "IGVFFI2799DOBT",
"aliases": [
"gary-hon:LW233C_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:24:16.850511+00:00",
"file_format": "fastq",
"file_size": 402049150,
"href": "/sequence-files/IGVFFI2799DOBT/@@download/IGVFFI2799DOBT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/5d1c94df-a4fe-4214-b486-e9ac44dbbb1e/IGVFFI2799DOBT.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/LW233C_S11_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6392CKYO/",
"accession": "IGVFFI6392CKYO",
"aliases": [
"gary-hon:LW233C_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:24:24.519762+00:00",
"file_format": "fastq",
"file_size": 745703827,
"href": "/sequence-files/IGVFFI6392CKYO/@@download/IGVFFI6392CKYO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/661300a2-0e9f-4c8b-b27d-e8056610cae7/IGVFFI6392CKYO.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/LW233C_S11_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/IGVFDS4323LXLZ/",
"accession": "IGVFDS4323LXLZ",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW233"
],
"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/IGVFSM9371INZC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9371INZC",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW233"
],
"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_LW263), 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": "2024-02-21T18:23:36.330004+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": "3f466030-a841-4eb9-a607-bf5bdfc3ea51"
}