{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS7783CMAZ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS7783CMAZ",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW261"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7783CMAZ](/auxiliary-sets/IGVFDS7783CMAZ/) has sequence file(s) [IGVFFI4960KIPY](/sequence-files/IGVFFI4960KIPY/), [IGVFFI0465HHKI](/sequence-files/IGVFFI0465HHKI/), [IGVFFI2358HDWU](/sequence-files/IGVFFI2358HDWU/), [IGVFFI0811GSLQ](/sequence-files/IGVFFI0811GSLQ/) 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/IGVFDS7783CMAZ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7783CMAZ](/auxiliary-sets/IGVFDS7783CMAZ/) has sequence file(s): [IGVFFI4960KIPY](/sequence-files/IGVFFI4960KIPY/), [IGVFFI0465HHKI](/sequence-files/IGVFFI0465HHKI/), [IGVFFI2358HDWU](/sequence-files/IGVFFI2358HDWU/), [IGVFFI0811GSLQ](/sequence-files/IGVFFI0811GSLQ/) 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/IGVFDS7783CMAZ/"
}
]
},
"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": "2024-02-15T23:35:49.402192+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/IGVFFI4960KIPY/",
"accession": "IGVFFI4960KIPY",
"aliases": [
"gary-hon:LW261C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:33:48.705103+00:00",
"file_format": "fastq",
"file_size": 94335986,
"href": "/sequence-files/IGVFFI4960KIPY/@@download/IGVFFI4960KIPY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/6e100dfa-8bfb-4866-92fc-e15dde686317/IGVFFI4960KIPY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-07-McDermott-NextSeq.10X.run1.sgRNA_HTO/2023-07-07/outs/fastq_path/AACV7CFM5/LW261C_S9_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0465HHKI/",
"accession": "IGVFFI0465HHKI",
"aliases": [
"gary-hon:LW261C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:33:58.831353+00:00",
"file_format": "fastq",
"file_size": 297550547,
"href": "/sequence-files/IGVFFI0465HHKI/@@download/IGVFFI0465HHKI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/fd9147e4-ef1e-41f4-b353-511ce00ad6b1/IGVFFI0465HHKI.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-07-McDermott-NextSeq.10X.run1.sgRNA_HTO/2023-07-07/outs/fastq_path/AACV7CFM5/LW261C_S9_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2358HDWU/",
"accession": "IGVFFI2358HDWU",
"aliases": [
"gary-hon:LW261C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:34:05.561625+00:00",
"file_format": "fastq",
"file_size": 764819979,
"href": "/sequence-files/IGVFFI2358HDWU/@@download/IGVFFI2358HDWU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/c0689c57-4244-410d-8016-4b3af36e37e0/IGVFFI2358HDWU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-07-McDermott-NextSeq.10X.run1.sgRNA_HTO/2023-07-07/outs/fastq_path/AACV7CFM5/LW261C_S9_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0811GSLQ/",
"accession": "IGVFFI0811GSLQ",
"aliases": [
"gary-hon:LW261C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:33:53.910419+00:00",
"file_format": "fastq",
"file_size": 96459449,
"href": "/sequence-files/IGVFFI0811GSLQ/@@download/IGVFFI0811GSLQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/fc37d6ea-0828-4313-95a9-6234fc28fa68/IGVFFI0811GSLQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-07-McDermott-NextSeq.10X.run1.sgRNA_HTO/2023-07-07/outs/fastq_path/AACV7CFM5/LW261C_S9_L001_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4003HZAB/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0262BREE/",
"accession": "IGVFDS0262BREE",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW261"
],
"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/IGVFSM1972EKCJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1972EKCJ",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW261"
],
"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_LW261), 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": "2024-02-20T20:33:48.705103+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": "267b4aa8-c7c2-48c3-b3f3-42e2949fdae1"
}