{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2612LSTD/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2612LSTD",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_sgRNA_LW281"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2612LSTD](/auxiliary-sets/IGVFDS2612LSTD/) has sequence file(s) [IGVFFI6611BGPK](/sequence-files/IGVFFI6611BGPK/), [IGVFFI4582VNCZ](/sequence-files/IGVFFI4582VNCZ/), [IGVFFI1807ZQQP](/sequence-files/IGVFFI1807ZQQP/), [IGVFFI6515ZKTF](/sequence-files/IGVFFI6515ZKTF/), [IGVFFI4919JJPZ](/sequence-files/IGVFFI4919JJPZ/), [IGVFFI8349NVKT](/sequence-files/IGVFFI8349NVKT/), [IGVFFI5164GGZB](/sequence-files/IGVFFI5164GGZB/), [IGVFFI4061QSKL](/sequence-files/IGVFFI4061QSKL/) 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/IGVFDS2612LSTD/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2612LSTD](/auxiliary-sets/IGVFDS2612LSTD/) has sequence file(s): [IGVFFI6611BGPK](/sequence-files/IGVFFI6611BGPK/), [IGVFFI4582VNCZ](/sequence-files/IGVFFI4582VNCZ/), [IGVFFI1807ZQQP](/sequence-files/IGVFFI1807ZQQP/), [IGVFFI6515ZKTF](/sequence-files/IGVFFI6515ZKTF/), [IGVFFI4919JJPZ](/sequence-files/IGVFFI4919JJPZ/), [IGVFFI8349NVKT](/sequence-files/IGVFFI8349NVKT/), [IGVFFI5164GGZB](/sequence-files/IGVFFI5164GGZB/), [IGVFFI4061QSKL](/sequence-files/IGVFFI4061QSKL/) 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/IGVFDS2612LSTD/"
}
]
},
"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": "2024-02-29T16:49:37.703831+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/IGVFFI6611BGPK/",
"accession": "IGVFFI6611BGPK",
"aliases": [
"gary-hon:LW281B-3_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:17:06.238498+00:00",
"file_format": "fastq",
"file_size": 586933448,
"href": "/sequence-files/IGVFFI6611BGPK/@@download/IGVFFI6611BGPK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/15e25596-3605-4c54-944f-cf7f1004e20e/IGVFFI6611BGPK.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/LW281B-3_S27_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4582VNCZ/",
"accession": "IGVFFI4582VNCZ",
"aliases": [
"gary-hon:LW281B-3_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:16:46.744625+00:00",
"file_format": "fastq",
"file_size": 193538045,
"href": "/sequence-files/IGVFFI4582VNCZ/@@download/IGVFFI4582VNCZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/c9e219ce-63ad-4bb9-b892-a3e82555837f/IGVFFI4582VNCZ.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/LW281B-3_S27_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1807ZQQP/",
"accession": "IGVFFI1807ZQQP",
"aliases": [
"gary-hon:LW281B-3_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:16:28.589903+00:00",
"file_format": "fastq",
"file_size": 582616929,
"href": "/sequence-files/IGVFFI1807ZQQP/@@download/IGVFFI1807ZQQP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/0e688549-7b9f-424a-8018-852825133dbc/IGVFFI1807ZQQP.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/LW281B-3_S27_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6515ZKTF/",
"accession": "IGVFFI6515ZKTF",
"aliases": [
"gary-hon:LW281B-3_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:16:23.329751+00:00",
"file_format": "fastq",
"file_size": 181647966,
"href": "/sequence-files/IGVFFI6515ZKTF/@@download/IGVFFI6515ZKTF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/d2924814-a516-40d2-8adb-3669f34c7192/IGVFFI6515ZKTF.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/LW281B-3_S27_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4919JJPZ/",
"accession": "IGVFFI4919JJPZ",
"aliases": [
"gary-hon:LW281B-3_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:16:37.919712+00:00",
"file_format": "fastq",
"file_size": 614190993,
"href": "/sequence-files/IGVFFI4919JJPZ/@@download/IGVFFI4919JJPZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/f9baa631-ca13-4779-8e87-48fdad0b1c37/IGVFFI4919JJPZ.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/LW281B-3_S27_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8349NVKT/",
"accession": "IGVFFI8349NVKT",
"aliases": [
"gary-hon:LW281B-3_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:16:17.730047+00:00",
"file_format": "fastq",
"file_size": 204112954,
"href": "/sequence-files/IGVFFI8349NVKT/@@download/IGVFFI8349NVKT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/d9578b2c-beaa-4c70-a433-67bc7e3fe8f3/IGVFFI8349NVKT.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/LW281B-3_S27_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5164GGZB/",
"accession": "IGVFFI5164GGZB",
"aliases": [
"gary-hon:LW281B-3_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:16:57.478554+00:00",
"file_format": "fastq",
"file_size": 563712755,
"href": "/sequence-files/IGVFFI5164GGZB/@@download/IGVFFI5164GGZB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/3211f4fa-fb32-4ba2-805c-e2487485fe02/IGVFFI5164GGZB.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/LW281B-3_S27_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4061QSKL/",
"accession": "IGVFFI4061QSKL",
"aliases": [
"gary-hon:LW281B-3_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:16:52.249456+00:00",
"file_format": "fastq",
"file_size": 173951364,
"href": "/sequence-files/IGVFFI4061QSKL/@@download/IGVFFI4061QSKL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/4d9995c0-5185-440a-8b89-ff90e271e739/IGVFFI4061QSKL.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/LW281B-3_S27_L002_I2_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"
}
],
"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": "2024-03-01T17:16:17.730047+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "39a74093-2660-47a2-9d6b-49eb043722bb"
}