{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6231TYIS/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6231TYIS",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_HTO_LW277"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6231TYIS](/auxiliary-sets/IGVFDS6231TYIS/) has sequence file(s) [IGVFFI3619XUDY](/sequence-files/IGVFFI3619XUDY/), [IGVFFI8623EMUX](/sequence-files/IGVFFI8623EMUX/), [IGVFFI7242OHQZ](/sequence-files/IGVFFI7242OHQZ/), [IGVFFI3194VIYW](/sequence-files/IGVFFI3194VIYW/), [IGVFFI6434GRPO](/sequence-files/IGVFFI6434GRPO/), [IGVFFI5716PBAK](/sequence-files/IGVFFI5716PBAK/), [IGVFFI2229JWQR](/sequence-files/IGVFFI2229JWQR/), [IGVFFI7413XGHD](/sequence-files/IGVFFI7413XGHD/) 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/IGVFDS6231TYIS/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6231TYIS](/auxiliary-sets/IGVFDS6231TYIS/) has sequence file(s): [IGVFFI3619XUDY](/sequence-files/IGVFFI3619XUDY/), [IGVFFI8623EMUX](/sequence-files/IGVFFI8623EMUX/), [IGVFFI7242OHQZ](/sequence-files/IGVFFI7242OHQZ/), [IGVFFI3194VIYW](/sequence-files/IGVFFI3194VIYW/), [IGVFFI6434GRPO](/sequence-files/IGVFFI6434GRPO/), [IGVFFI5716PBAK](/sequence-files/IGVFFI5716PBAK/), [IGVFFI2229JWQR](/sequence-files/IGVFFI2229JWQR/), [IGVFFI7413XGHD](/sequence-files/IGVFFI7413XGHD/) 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/IGVFDS6231TYIS/"
}
]
},
"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": "2024-02-21T21:01:47.038154+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/IGVFFI3619XUDY/",
"accession": "IGVFFI3619XUDY",
"aliases": [
"gary-hon:LW277C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:06:52.909453+00:00",
"file_format": "fastq",
"file_size": 68254695,
"href": "/sequence-files/IGVFFI3619XUDY/@@download/IGVFFI3619XUDY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/8d26c1bb-851e-4af2-b0d8-621293c78421/IGVFFI3619XUDY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW277C_S1_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8623EMUX/",
"accession": "IGVFFI8623EMUX",
"aliases": [
"gary-hon:LW277C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:07:06.417870+00:00",
"file_format": "fastq",
"file_size": 199741054,
"href": "/sequence-files/IGVFFI8623EMUX/@@download/IGVFFI8623EMUX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/19b79176-48b4-42d9-a749-2ae4b4330e58/IGVFFI8623EMUX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW277C_S1_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7242OHQZ/",
"accession": "IGVFFI7242OHQZ",
"aliases": [
"gary-hon:LW277C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:07:12.203973+00:00",
"file_format": "fastq",
"file_size": 399339537,
"href": "/sequence-files/IGVFFI7242OHQZ/@@download/IGVFFI7242OHQZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/bbfc27fc-79e6-4b93-a7e8-68acfa6949b4/IGVFFI7242OHQZ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW277C_S1_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3194VIYW/",
"accession": "IGVFFI3194VIYW",
"aliases": [
"gary-hon:LW277C_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:07:28.287364+00:00",
"file_format": "fastq",
"file_size": 179466961,
"href": "/sequence-files/IGVFFI3194VIYW/@@download/IGVFFI3194VIYW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/4d58824c-17b4-45ca-ab10-6bc8c266fa17/IGVFFI3194VIYW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW277C_S1_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6434GRPO/",
"accession": "IGVFFI6434GRPO",
"aliases": [
"gary-hon:LW277C_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:07:23.782790+00:00",
"file_format": "fastq",
"file_size": 72831186,
"href": "/sequence-files/IGVFFI6434GRPO/@@download/IGVFFI6434GRPO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/add8b66f-fc45-4a6f-a017-f4af5fcd8071/IGVFFI6434GRPO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW277C_S1_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5716PBAK/",
"accession": "IGVFFI5716PBAK",
"aliases": [
"gary-hon:LW277C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:06:57.394000+00:00",
"file_format": "fastq",
"file_size": 80839978,
"href": "/sequence-files/IGVFFI5716PBAK/@@download/IGVFFI5716PBAK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/b21cd38c-64aa-4932-956b-680dab9bd205/IGVFFI5716PBAK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW277C_S1_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2229JWQR/",
"accession": "IGVFFI2229JWQR",
"aliases": [
"gary-hon:LW277C_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:07:19.314859+00:00",
"file_format": "fastq",
"file_size": 61957129,
"href": "/sequence-files/IGVFFI2229JWQR/@@download/IGVFFI2229JWQR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/ac077c32-fabc-413b-a38f-6b0c6ceac1fb/IGVFFI2229JWQR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW277C_S1_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7413XGHD/",
"accession": "IGVFFI7413XGHD",
"aliases": [
"gary-hon:LW277C_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:07:33.734526+00:00",
"file_format": "fastq",
"file_size": 357595322,
"href": "/sequence-files/IGVFFI7413XGHD/@@download/IGVFFI7413XGHD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/712a7f8e-a35b-4156-aadf-e7a2f610113f/IGVFFI7413XGHD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW277C_S1_L002_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4389OUWU/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS7834BXBN/",
"accession": "IGVFDS7834BXBN",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_LW277"
],
"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/IGVFSM7513BJDT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7513BJDT",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti_LW277"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS2302LCEO/"
],
"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_LW277), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) 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": "2024-03-01T17:06:52.909453+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": "c78b337c-cb4b-4260-9cef-6996b8b40a59"
}