{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2693DPLW/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2693DPLW",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_HTO_LW284"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2693DPLW](/auxiliary-sets/IGVFDS2693DPLW/) has sequence file(s) [IGVFFI7707CNCP](/sequence-files/IGVFFI7707CNCP/), [IGVFFI7180TCQN](/sequence-files/IGVFFI7180TCQN/), [IGVFFI4098UEYI](/sequence-files/IGVFFI4098UEYI/), [IGVFFI0338ZIDU](/sequence-files/IGVFFI0338ZIDU/), [IGVFFI2183YERZ](/sequence-files/IGVFFI2183YERZ/), [IGVFFI2451CCHU](/sequence-files/IGVFFI2451CCHU/), [IGVFFI7688VJBW](/sequence-files/IGVFFI7688VJBW/), [IGVFFI7643DOED](/sequence-files/IGVFFI7643DOED/) 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/IGVFDS2693DPLW/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2693DPLW](/auxiliary-sets/IGVFDS2693DPLW/) has sequence file(s): [IGVFFI7707CNCP](/sequence-files/IGVFFI7707CNCP/), [IGVFFI7180TCQN](/sequence-files/IGVFFI7180TCQN/), [IGVFFI4098UEYI](/sequence-files/IGVFFI4098UEYI/), [IGVFFI0338ZIDU](/sequence-files/IGVFFI0338ZIDU/), [IGVFFI2183YERZ](/sequence-files/IGVFFI2183YERZ/), [IGVFFI2451CCHU](/sequence-files/IGVFFI2451CCHU/), [IGVFFI7688VJBW](/sequence-files/IGVFFI7688VJBW/), [IGVFFI7643DOED](/sequence-files/IGVFFI7643DOED/) 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/IGVFDS2693DPLW/"
}
]
},
"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": "2024-02-29T16:49:46.907832+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/IGVFFI7707CNCP/",
"accession": "IGVFFI7707CNCP",
"aliases": [
"gary-hon:LW284C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:25:15.703000+00:00",
"file_format": "fastq",
"file_size": 91759907,
"href": "/sequence-files/IGVFFI7707CNCP/@@download/IGVFFI7707CNCP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/3c8502d3-5e73-4db3-8189-a9fadb70418a/IGVFFI7707CNCP.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/LW284C_S8_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7180TCQN/",
"accession": "IGVFFI7180TCQN",
"aliases": [
"gary-hon:LW284C_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:25:38.326273+00:00",
"file_format": "fastq",
"file_size": 85494456,
"href": "/sequence-files/IGVFFI7180TCQN/@@download/IGVFFI7180TCQN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/be74d241-9347-43a7-ae60-3a8e5fb56cbb/IGVFFI7180TCQN.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/LW284C_S8_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4098UEYI/",
"accession": "IGVFFI4098UEYI",
"aliases": [
"gary-hon:LW284C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:25:11.208615+00:00",
"file_format": "fastq",
"file_size": 86751835,
"href": "/sequence-files/IGVFFI4098UEYI/@@download/IGVFFI4098UEYI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/e064fdbe-adde-497d-b959-541cc528a497/IGVFFI4098UEYI.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/LW284C_S8_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0338ZIDU/",
"accession": "IGVFFI0338ZIDU",
"aliases": [
"gary-hon:LW284C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:25:20.198825+00:00",
"file_format": "fastq",
"file_size": 230341722,
"href": "/sequence-files/IGVFFI0338ZIDU/@@download/IGVFFI0338ZIDU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/ff289dd6-6da1-4a65-bc61-1f6781746c91/IGVFFI0338ZIDU.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/LW284C_S8_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2183YERZ/",
"accession": "IGVFFI2183YERZ",
"aliases": [
"gary-hon:LW284C_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:25:42.901555+00:00",
"file_format": "fastq",
"file_size": 212255885,
"href": "/sequence-files/IGVFFI2183YERZ/@@download/IGVFFI2183YERZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/cd7655f9-a31b-4cb6-83b2-70684c0804f7/IGVFFI2183YERZ.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/LW284C_S8_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2451CCHU/",
"accession": "IGVFFI2451CCHU",
"aliases": [
"gary-hon:LW284C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:25:26.044216+00:00",
"file_format": "fastq",
"file_size": 454494709,
"href": "/sequence-files/IGVFFI2451CCHU/@@download/IGVFFI2451CCHU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/4712de2b-1f3c-42c1-92be-f4be5f4b9fb9/IGVFFI2451CCHU.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/LW284C_S8_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7688VJBW/",
"accession": "IGVFFI7688VJBW",
"aliases": [
"gary-hon:LW284C_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:25:33.764630+00:00",
"file_format": "fastq",
"file_size": 79419413,
"href": "/sequence-files/IGVFFI7688VJBW/@@download/IGVFFI7688VJBW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/49510059-2636-475d-96a0-1924d3762e83/IGVFFI7688VJBW.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/LW284C_S8_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7643DOED/",
"accession": "IGVFFI7643DOED",
"aliases": [
"gary-hon:LW284C_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:25:48.480356+00:00",
"file_format": "fastq",
"file_size": 416376794,
"href": "/sequence-files/IGVFFI7643DOED/@@download/IGVFFI7643DOED.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/33ebc747-4d34-4253-8a01-d441a7fce2a3/IGVFFI7643DOED.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/LW284C_S8_L002_R2_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/IGVFDS0657YBVN/",
"accession": "IGVFDS0657YBVN",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW284"
],
"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/IGVFSM2597WGYB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2597WGYB",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW284"
],
"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_LW284), 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": "2024-03-01T17:25:11.208615+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": "389826a6-e9fe-4a5f-92a3-eec57ccf9ad8"
}