{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS0109SCQO/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0109SCQO",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_HTO_LW278"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0109SCQO](/auxiliary-sets/IGVFDS0109SCQO/) has sequence file(s) [IGVFFI0359OPZH](/sequence-files/IGVFFI0359OPZH/), [IGVFFI1587BLSX](/sequence-files/IGVFFI1587BLSX/), [IGVFFI8395IXDC](/sequence-files/IGVFFI8395IXDC/), [IGVFFI6340VLIA](/sequence-files/IGVFFI6340VLIA/), [IGVFFI5123HTNM](/sequence-files/IGVFFI5123HTNM/), [IGVFFI5460OSRQ](/sequence-files/IGVFFI5460OSRQ/), [IGVFFI6913WKOH](/sequence-files/IGVFFI6913WKOH/), [IGVFFI3244CIGW](/sequence-files/IGVFFI3244CIGW/) 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/IGVFDS0109SCQO/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0109SCQO](/auxiliary-sets/IGVFDS0109SCQO/) has sequence file(s): [IGVFFI0359OPZH](/sequence-files/IGVFFI0359OPZH/), [IGVFFI1587BLSX](/sequence-files/IGVFFI1587BLSX/), [IGVFFI8395IXDC](/sequence-files/IGVFFI8395IXDC/), [IGVFFI6340VLIA](/sequence-files/IGVFFI6340VLIA/), [IGVFFI5123HTNM](/sequence-files/IGVFFI5123HTNM/), [IGVFFI5460OSRQ](/sequence-files/IGVFFI5460OSRQ/), [IGVFFI6913WKOH](/sequence-files/IGVFFI6913WKOH/), [IGVFFI3244CIGW](/sequence-files/IGVFFI3244CIGW/) 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/IGVFDS0109SCQO/"
}
]
},
"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": "2024-02-21T21:01:49.698804+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/IGVFFI0359OPZH/",
"accession": "IGVFFI0359OPZH",
"aliases": [
"gary-hon:LW278C_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:09:53.761423+00:00",
"file_format": "fastq",
"file_size": 97192698,
"href": "/sequence-files/IGVFFI0359OPZH/@@download/IGVFFI0359OPZH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/be5459fc-24cc-4b67-9992-dd7980ecc956/IGVFFI0359OPZH.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/LW278C_S2_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1587BLSX/",
"accession": "IGVFFI1587BLSX",
"aliases": [
"gary-hon:LW278C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:09:45.489821+00:00",
"file_format": "fastq",
"file_size": 522117032,
"href": "/sequence-files/IGVFFI1587BLSX/@@download/IGVFFI1587BLSX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/ffc16f3a-a901-4f55-9094-a290474e5f74/IGVFFI1587BLSX.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/LW278C_S2_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8395IXDC/",
"accession": "IGVFFI8395IXDC",
"aliases": [
"gary-hon:LW278C_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:10:03.390409+00:00",
"file_format": "fastq",
"file_size": 241724077,
"href": "/sequence-files/IGVFFI8395IXDC/@@download/IGVFFI8395IXDC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/820b3cbe-f5d9-4545-b9f7-249d56bdcbfd/IGVFFI8395IXDC.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/LW278C_S2_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6340VLIA/",
"accession": "IGVFFI6340VLIA",
"aliases": [
"gary-hon:LW278C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:09:29.477111+00:00",
"file_format": "fastq",
"file_size": 105931695,
"href": "/sequence-files/IGVFFI6340VLIA/@@download/IGVFFI6340VLIA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/3fa4af1c-ddb2-4e96-bfc7-454774c5dd69/IGVFFI6340VLIA.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/LW278C_S2_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5123HTNM/",
"accession": "IGVFFI5123HTNM",
"aliases": [
"gary-hon:LW278C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:09:34.567215+00:00",
"file_format": "fastq",
"file_size": 105602901,
"href": "/sequence-files/IGVFFI5123HTNM/@@download/IGVFFI5123HTNM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/c06af458-5ac9-4010-940a-552fc52a7a0e/IGVFFI5123HTNM.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/LW278C_S2_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5460OSRQ/",
"accession": "IGVFFI5460OSRQ",
"aliases": [
"gary-hon:LW278C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:09:39.479395+00:00",
"file_format": "fastq",
"file_size": 269138498,
"href": "/sequence-files/IGVFFI5460OSRQ/@@download/IGVFFI5460OSRQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/3fae8a4b-3b2a-4d75-a49c-660b91120b89/IGVFFI5460OSRQ.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/LW278C_S2_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6913WKOH/",
"accession": "IGVFFI6913WKOH",
"aliases": [
"gary-hon:LW278C_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:09:58.520370+00:00",
"file_format": "fastq",
"file_size": 89648633,
"href": "/sequence-files/IGVFFI6913WKOH/@@download/IGVFFI6913WKOH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/bec507f9-a304-4953-b61a-93aa2047e6f9/IGVFFI6913WKOH.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/LW278C_S2_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3244CIGW/",
"accession": "IGVFFI3244CIGW",
"aliases": [
"gary-hon:LW278C_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:10:09.316437+00:00",
"file_format": "fastq",
"file_size": 468158521,
"href": "/sequence-files/IGVFFI3244CIGW/@@download/IGVFFI3244CIGW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/05d35361-1c4a-40ed-8473-337fffe163ef/IGVFFI3244CIGW.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/LW278C_S2_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/IGVFDS2628PYOH/",
"accession": "IGVFDS2628PYOH",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_LW278"
],
"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/IGVFSM7499ZWUW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7499ZWUW",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti_LW278"
],
"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_LW278), 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": "2024-03-01T17:09:29.477111+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": "c621f91a-4614-4382-9096-10b4be8a944b"
}