{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2549GCKW/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2549GCKW",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_HTO_LW281"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2549GCKW](/auxiliary-sets/IGVFDS2549GCKW/) has sequence file(s) [IGVFFI4327UMKJ](/sequence-files/IGVFFI4327UMKJ/), [IGVFFI3275IUJQ](/sequence-files/IGVFFI3275IUJQ/), [IGVFFI0782ZJOJ](/sequence-files/IGVFFI0782ZJOJ/), [IGVFFI0713WITI](/sequence-files/IGVFFI0713WITI/), [IGVFFI4515BKOL](/sequence-files/IGVFFI4515BKOL/), [IGVFFI2642JAIF](/sequence-files/IGVFFI2642JAIF/), [IGVFFI8312SSMA](/sequence-files/IGVFFI8312SSMA/), [IGVFFI5462TUJG](/sequence-files/IGVFFI5462TUJG/) 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/IGVFDS2549GCKW/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2549GCKW](/auxiliary-sets/IGVFDS2549GCKW/) has sequence file(s): [IGVFFI4327UMKJ](/sequence-files/IGVFFI4327UMKJ/), [IGVFFI3275IUJQ](/sequence-files/IGVFFI3275IUJQ/), [IGVFFI0782ZJOJ](/sequence-files/IGVFFI0782ZJOJ/), [IGVFFI0713WITI](/sequence-files/IGVFFI0713WITI/), [IGVFFI4515BKOL](/sequence-files/IGVFFI4515BKOL/), [IGVFFI2642JAIF](/sequence-files/IGVFFI2642JAIF/), [IGVFFI8312SSMA](/sequence-files/IGVFFI8312SSMA/), [IGVFFI5462TUJG](/sequence-files/IGVFFI5462TUJG/) 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/IGVFDS2549GCKW/"
}
]
},
"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": "2024-02-29T16:49:38.928501+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/IGVFFI4327UMKJ/",
"accession": "IGVFFI4327UMKJ",
"aliases": [
"gary-hon:LW281C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:17:19.802636+00:00",
"file_format": "fastq",
"file_size": 92006323,
"href": "/sequence-files/IGVFFI4327UMKJ/@@download/IGVFFI4327UMKJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/d935103c-8802-4a09-b869-d16ab6ed99b1/IGVFFI4327UMKJ.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/LW281C_S5_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3275IUJQ/",
"accession": "IGVFFI3275IUJQ",
"aliases": [
"gary-hon:LW281C_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:17:52.292101+00:00",
"file_format": "fastq",
"file_size": 412025496,
"href": "/sequence-files/IGVFFI3275IUJQ/@@download/IGVFFI3275IUJQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/4ec9c7e0-5dea-4fc8-99d2-891473f9b5ed/IGVFFI3275IUJQ.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/LW281C_S5_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0782ZJOJ/",
"accession": "IGVFFI0782ZJOJ",
"aliases": [
"gary-hon:LW281C_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:17:42.184096+00:00",
"file_format": "fastq",
"file_size": 83174381,
"href": "/sequence-files/IGVFFI0782ZJOJ/@@download/IGVFFI0782ZJOJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/13510e77-6db6-4f03-973a-2beb5e89cee8/IGVFFI0782ZJOJ.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/LW281C_S5_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0713WITI/",
"accession": "IGVFFI0713WITI",
"aliases": [
"gary-hon:LW281C_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:17:46.726464+00:00",
"file_format": "fastq",
"file_size": 207256719,
"href": "/sequence-files/IGVFFI0713WITI/@@download/IGVFFI0713WITI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/ef6de3f5-2f85-4639-996b-94c3297caab3/IGVFFI0713WITI.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/LW281C_S5_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4515BKOL/",
"accession": "IGVFFI4515BKOL",
"aliases": [
"gary-hon:LW281C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:17:15.336869+00:00",
"file_format": "fastq",
"file_size": 82361172,
"href": "/sequence-files/IGVFFI4515BKOL/@@download/IGVFFI4515BKOL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/89ba43b8-5687-4258-8006-ecc9ec6f5820/IGVFFI4515BKOL.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/LW281C_S5_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2642JAIF/",
"accession": "IGVFFI2642JAIF",
"aliases": [
"gary-hon:LW281C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:17:24.355923+00:00",
"file_format": "fastq",
"file_size": 231903639,
"href": "/sequence-files/IGVFFI2642JAIF/@@download/IGVFFI2642JAIF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/b774cdba-13b9-4f64-aea0-dad698dfab2a/IGVFFI2642JAIF.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/LW281C_S5_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8312SSMA/",
"accession": "IGVFFI8312SSMA",
"aliases": [
"gary-hon:LW281C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:17:30.017669+00:00",
"file_format": "fastq",
"file_size": 465008328,
"href": "/sequence-files/IGVFFI8312SSMA/@@download/IGVFFI8312SSMA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/647e7ff8-639b-4517-9670-8d8f96c47e39/IGVFFI8312SSMA.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/LW281C_S5_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5462TUJG/",
"accession": "IGVFFI5462TUJG",
"aliases": [
"gary-hon:LW281C_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:17:37.694937+00:00",
"file_format": "fastq",
"file_size": 75510756,
"href": "/sequence-files/IGVFFI5462TUJG/@@download/IGVFFI5462TUJG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/cf1b4508-2f3c-4aef-9cc8-13eabd44e7ed/IGVFFI5462TUJG.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/LW281C_S5_L002_I1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1588TVKF/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2143BSOH/",
"accession": "IGVFDS2143BSOH",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW281"
],
"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/IGVFSM0956HKRJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0956HKRJ",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW281"
],
"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 neural stem cell for 20 days (cellular sub pool: subpool_LW281), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000047/",
"status": "preview",
"term_name": "neural stem cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-03-01T17:17:15.336869+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": "bdfdaa2e-97ab-4ee0-ac79-935187bfed55"
}