{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2373RGIJ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2373RGIJ",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_HTO_LW287"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2373RGIJ](/auxiliary-sets/IGVFDS2373RGIJ/) has sequence file(s) [IGVFFI7050AVQG](/sequence-files/IGVFFI7050AVQG/), [IGVFFI6282MCFD](/sequence-files/IGVFFI6282MCFD/), [IGVFFI5493BBTV](/sequence-files/IGVFFI5493BBTV/), [IGVFFI1454KXNR](/sequence-files/IGVFFI1454KXNR/) 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/IGVFDS2373RGIJ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2373RGIJ](/auxiliary-sets/IGVFDS2373RGIJ/) has sequence file(s): [IGVFFI7050AVQG](/sequence-files/IGVFFI7050AVQG/), [IGVFFI6282MCFD](/sequence-files/IGVFFI6282MCFD/), [IGVFFI5493BBTV](/sequence-files/IGVFFI5493BBTV/), [IGVFFI1454KXNR](/sequence-files/IGVFFI1454KXNR/) 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/IGVFDS2373RGIJ/"
}
]
},
"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": "2024-02-21T21:22:40.659393+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/IGVFFI7050AVQG/",
"accession": "IGVFFI7050AVQG",
"aliases": [
"gary-hon:LW287C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:04:49.096182+00:00",
"file_format": "fastq",
"file_size": 104345442,
"href": "/sequence-files/IGVFFI7050AVQG/@@download/IGVFFI7050AVQG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/3c49a80e-e485-4b38-9bf6-fe779812d836/IGVFFI7050AVQG.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run2.10X/2023-11-03/outs/fastq_path/AAF3JCVM5//LW287C_S6_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6282MCFD/",
"accession": "IGVFFI6282MCFD",
"aliases": [
"gary-hon:LW287C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:04:53.931571+00:00",
"file_format": "fastq",
"file_size": 113086803,
"href": "/sequence-files/IGVFFI6282MCFD/@@download/IGVFFI6282MCFD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/00ea7640-88c6-4cc4-a88d-d8b743519976/IGVFFI6282MCFD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run2.10X/2023-11-03/outs/fastq_path/AAF3JCVM5//LW287C_S6_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5493BBTV/",
"accession": "IGVFFI5493BBTV",
"aliases": [
"gary-hon:LW287C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:04:58.935025+00:00",
"file_format": "fastq",
"file_size": 309631559,
"href": "/sequence-files/IGVFFI5493BBTV/@@download/IGVFFI5493BBTV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/c2990a42-ce29-4d4c-a4a6-bd503b9048b8/IGVFFI5493BBTV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run2.10X/2023-11-03/outs/fastq_path/AAF3JCVM5//LW287C_S6_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1454KXNR/",
"accession": "IGVFFI1454KXNR",
"aliases": [
"gary-hon:LW287C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T20:05:05.588642+00:00",
"file_format": "fastq",
"file_size": 622014781,
"href": "/sequence-files/IGVFFI1454KXNR/@@download/IGVFFI1454KXNR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/f6458399-0136-4dfe-b944-50a0c20ece75/IGVFFI1454KXNR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run2.10X/2023-11-03/outs/fastq_path/AAF3JCVM5//LW287C_S6_L001_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7340YDHF/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2692VBHQ/",
"accession": "IGVFDS2692VBHQ",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_LW287"
],
"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/IGVFSM1153INDY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1153INDY",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW287"
],
"classifications": [
"cell line"
],
"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) cell line (cellular sub pool: subpool_LW287), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-03-04T20:04:49.096182+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": "91af8b07-0ae2-4df2-8128-271a45c29f29"
}