{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6861GRJI/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6861GRJI",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_sgRNA_LW280"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6861GRJI](/auxiliary-sets/IGVFDS6861GRJI/) has sequence file(s) [IGVFFI7902JDLP](/sequence-files/IGVFFI7902JDLP/), [IGVFFI5920ILPO](/sequence-files/IGVFFI5920ILPO/), [IGVFFI0148GGAF](/sequence-files/IGVFFI0148GGAF/), [IGVFFI9772UXBJ](/sequence-files/IGVFFI9772UXBJ/), [IGVFFI5059JEYE](/sequence-files/IGVFFI5059JEYE/), [IGVFFI4378HMYC](/sequence-files/IGVFFI4378HMYC/), [IGVFFI7335PJUM](/sequence-files/IGVFFI7335PJUM/), [IGVFFI2706WHPV](/sequence-files/IGVFFI2706WHPV/) 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/IGVFDS6861GRJI/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6861GRJI](/auxiliary-sets/IGVFDS6861GRJI/) has sequence file(s): [IGVFFI7902JDLP](/sequence-files/IGVFFI7902JDLP/), [IGVFFI5920ILPO](/sequence-files/IGVFFI5920ILPO/), [IGVFFI0148GGAF](/sequence-files/IGVFFI0148GGAF/), [IGVFFI9772UXBJ](/sequence-files/IGVFFI9772UXBJ/), [IGVFFI5059JEYE](/sequence-files/IGVFFI5059JEYE/), [IGVFFI4378HMYC](/sequence-files/IGVFFI4378HMYC/), [IGVFFI7335PJUM](/sequence-files/IGVFFI7335PJUM/), [IGVFFI2706WHPV](/sequence-files/IGVFFI2706WHPV/) 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/IGVFDS6861GRJI/"
}
]
},
"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": "2024-02-21T21:01:53.076003+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI7902JDLP/",
"accession": "IGVFFI7902JDLP",
"aliases": [
"gary-hon:LW280B-3_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:14:00.780118+00:00",
"file_format": "fastq",
"file_size": 574857973,
"href": "/sequence-files/IGVFFI7902JDLP/@@download/IGVFFI7902JDLP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/8dc5129a-e194-44d1-9990-800f81c53768/IGVFFI7902JDLP.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/LW280B-3_S26_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5920ILPO/",
"accession": "IGVFFI5920ILPO",
"aliases": [
"gary-hon:LW280B-3_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:14:18.736075+00:00",
"file_format": "fastq",
"file_size": 173082337,
"href": "/sequence-files/IGVFFI5920ILPO/@@download/IGVFFI5920ILPO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/bdcbbd11-7238-44f6-a8b1-3a6edd01e965/IGVFFI5920ILPO.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/LW280B-3_S26_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0148GGAF/",
"accession": "IGVFFI0148GGAF",
"aliases": [
"gary-hon:LW280B-3_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:14:29.371633+00:00",
"file_format": "fastq",
"file_size": 540790425,
"href": "/sequence-files/IGVFFI0148GGAF/@@download/IGVFFI0148GGAF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/4a61acc3-eae7-42da-8f87-1490a1c57acf/IGVFFI0148GGAF.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/LW280B-3_S26_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9772UXBJ/",
"accession": "IGVFFI9772UXBJ",
"aliases": [
"gary-hon:LW280B-3_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:13:55.279749+00:00",
"file_format": "fastq",
"file_size": 205377714,
"href": "/sequence-files/IGVFFI9772UXBJ/@@download/IGVFFI9772UXBJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/41953734-d20d-4fbf-ab8f-3356a448b52d/IGVFFI9772UXBJ.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/LW280B-3_S26_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5059JEYE/",
"accession": "IGVFFI5059JEYE",
"aliases": [
"gary-hon:LW280B-3_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:14:23.909156+00:00",
"file_format": "fastq",
"file_size": 189074016,
"href": "/sequence-files/IGVFFI5059JEYE/@@download/IGVFFI5059JEYE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/10df6f29-0bc4-4e12-b697-efd75dc8723d/IGVFFI5059JEYE.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/LW280B-3_S26_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4378HMYC/",
"accession": "IGVFFI4378HMYC",
"aliases": [
"gary-hon:LW280B-3_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:14:37.625153+00:00",
"file_format": "fastq",
"file_size": 577388001,
"href": "/sequence-files/IGVFFI4378HMYC/@@download/IGVFFI4378HMYC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/ea7362c0-47cc-45f8-8ac8-6c653e3e3bc4/IGVFFI4378HMYC.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/LW280B-3_S26_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7335PJUM/",
"accession": "IGVFFI7335PJUM",
"aliases": [
"gary-hon:LW280B-3_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:14:09.490092+00:00",
"file_format": "fastq",
"file_size": 621228332,
"href": "/sequence-files/IGVFFI7335PJUM/@@download/IGVFFI7335PJUM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/b09cfa17-7909-4be9-8e58-15a5a392daa9/IGVFFI7335PJUM.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/LW280B-3_S26_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2706WHPV/",
"accession": "IGVFFI2706WHPV",
"aliases": [
"gary-hon:LW280B-3_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:13:49.695132+00:00",
"file_format": "fastq",
"file_size": 193151174,
"href": "/sequence-files/IGVFFI2706WHPV/@@download/IGVFFI2706WHPV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/1345809f-aa4f-43e6-85f2-08726b4a08d3/IGVFFI2706WHPV.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/LW280B-3_S26_L001_I1_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/IGVFDS4852MAUM/",
"accession": "IGVFDS4852MAUM",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_LW280"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0604KDJF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0604KDJF",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti_LW280"
],
"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_LW280), 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": "2024-03-01T17:13:49.695132+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "51e97263-345f-4299-91d5-4b9ef2adc2df"
}