{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS0588CNDW/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0588CNDW",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW234"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0588CNDW](/auxiliary-sets/IGVFDS0588CNDW/) has sequence file(s) [IGVFFI5260PVLB](/sequence-files/IGVFFI5260PVLB/), [IGVFFI3175IIRZ](/sequence-files/IGVFFI3175IIRZ/), [IGVFFI2983OMXA](/sequence-files/IGVFFI2983OMXA/), [IGVFFI5434BAFC](/sequence-files/IGVFFI5434BAFC/), [IGVFFI9887KSTI](/sequence-files/IGVFFI9887KSTI/), [IGVFFI1014YNGM](/sequence-files/IGVFFI1014YNGM/), [IGVFFI9069TRUT](/sequence-files/IGVFFI9069TRUT/), [IGVFFI9904QNFV](/sequence-files/IGVFFI9904QNFV/) 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/IGVFDS0588CNDW/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0588CNDW](/auxiliary-sets/IGVFDS0588CNDW/) has sequence file(s): [IGVFFI5260PVLB](/sequence-files/IGVFFI5260PVLB/), [IGVFFI3175IIRZ](/sequence-files/IGVFFI3175IIRZ/), [IGVFFI2983OMXA](/sequence-files/IGVFFI2983OMXA/), [IGVFFI5434BAFC](/sequence-files/IGVFFI5434BAFC/), [IGVFFI9887KSTI](/sequence-files/IGVFFI9887KSTI/), [IGVFFI1014YNGM](/sequence-files/IGVFFI1014YNGM/), [IGVFFI9069TRUT](/sequence-files/IGVFFI9069TRUT/), [IGVFFI9904QNFV](/sequence-files/IGVFFI9904QNFV/) 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/IGVFDS0588CNDW/"
}
]
},
"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": "2024-02-15T23:35:37.502908+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/IGVFFI5260PVLB/",
"accession": "IGVFFI5260PVLB",
"aliases": [
"gary-hon:LW234C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:26:13.381500+00:00",
"file_format": "fastq",
"file_size": 410698654,
"href": "/sequence-files/IGVFFI5260PVLB/@@download/IGVFFI5260PVLB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/b967df60-1a37-48e3-8574-356a29904719/IGVFFI5260PVLB.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/LW234C_S12_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3175IIRZ/",
"accession": "IGVFFI3175IIRZ",
"aliases": [
"gary-hon:LW234C_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:26:47.626287+00:00",
"file_format": "fastq",
"file_size": 375239651,
"href": "/sequence-files/IGVFFI3175IIRZ/@@download/IGVFFI3175IIRZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/6fa36c40-89ce-4b8b-b190-d8733b346efb/IGVFFI3175IIRZ.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/LW234C_S12_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2983OMXA/",
"accession": "IGVFFI2983OMXA",
"aliases": [
"gary-hon:LW234C_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:26:55.071790+00:00",
"file_format": "fastq",
"file_size": 689646399,
"href": "/sequence-files/IGVFFI2983OMXA/@@download/IGVFFI2983OMXA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/4af73d73-f592-476e-bd02-a7e3121977a1/IGVFFI2983OMXA.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/LW234C_S12_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5434BAFC/",
"accession": "IGVFFI5434BAFC",
"aliases": [
"gary-hon:LW234C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:26:07.911894+00:00",
"file_format": "fastq",
"file_size": 138970043,
"href": "/sequence-files/IGVFFI5434BAFC/@@download/IGVFFI5434BAFC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/aedfeff3-dc19-402d-8ab6-75b63b02b679/IGVFFI5434BAFC.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/LW234C_S12_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9887KSTI/",
"accession": "IGVFFI9887KSTI",
"aliases": [
"gary-hon:LW234C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:26:02.378094+00:00",
"file_format": "fastq",
"file_size": 149393493,
"href": "/sequence-files/IGVFFI9887KSTI/@@download/IGVFFI9887KSTI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/2cf842d8-8492-46d3-aa18-1f19698c2031/IGVFFI9887KSTI.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/LW234C_S12_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1014YNGM/",
"accession": "IGVFFI1014YNGM",
"aliases": [
"gary-hon:LW234C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:26:20.848918+00:00",
"file_format": "fastq",
"file_size": 758495849,
"href": "/sequence-files/IGVFFI1014YNGM/@@download/IGVFFI1014YNGM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/7cfccf38-b854-4789-8b2f-08de58af6c85/IGVFFI1014YNGM.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/LW234C_S12_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9069TRUT/",
"accession": "IGVFFI9069TRUT",
"aliases": [
"gary-hon:LW234C_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:26:31.496950+00:00",
"file_format": "fastq",
"file_size": 134840670,
"href": "/sequence-files/IGVFFI9069TRUT/@@download/IGVFFI9069TRUT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/d48baf5d-ea82-4297-a571-49e93d3b804f/IGVFFI9069TRUT.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/LW234C_S12_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9904QNFV/",
"accession": "IGVFFI9904QNFV",
"aliases": [
"gary-hon:LW234C_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:26:37.084389+00:00",
"file_format": "fastq",
"file_size": 123261044,
"href": "/sequence-files/IGVFFI9904QNFV/@@download/IGVFFI9904QNFV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/720a455c-5652-4356-b3ca-15ff14a5285a/IGVFFI9904QNFV.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/LW234C_S12_L002_I2_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/IGVFDS8705MRYI/",
"accession": "IGVFDS8705MRYI",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW234"
],
"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/IGVFSM8137TZJW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8137TZJW",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW234"
],
"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_LW264), 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": "2024-02-21T18:26:02.378094+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": "e6f9c65a-1ecf-48b8-9770-fc09003bbe9e"
}