{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS2600XYHD/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2600XYHD",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_HTO_LW283"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2600XYHD](/auxiliary-sets/IGVFDS2600XYHD/) has sequence file(s) [IGVFFI5245DMCW](/sequence-files/IGVFFI5245DMCW/), [IGVFFI3918UPES](/sequence-files/IGVFFI3918UPES/), [IGVFFI7518XBAK](/sequence-files/IGVFFI7518XBAK/), [IGVFFI9972BHWI](/sequence-files/IGVFFI9972BHWI/), [IGVFFI8032BRVG](/sequence-files/IGVFFI8032BRVG/), [IGVFFI6392ULTE](/sequence-files/IGVFFI6392ULTE/), [IGVFFI2868ZCYM](/sequence-files/IGVFFI2868ZCYM/), [IGVFFI9747MXBT](/sequence-files/IGVFFI9747MXBT/) 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/IGVFDS2600XYHD/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2600XYHD](/auxiliary-sets/IGVFDS2600XYHD/) has sequence file(s): [IGVFFI5245DMCW](/sequence-files/IGVFFI5245DMCW/), [IGVFFI3918UPES](/sequence-files/IGVFFI3918UPES/), [IGVFFI7518XBAK](/sequence-files/IGVFFI7518XBAK/), [IGVFFI9972BHWI](/sequence-files/IGVFFI9972BHWI/), [IGVFFI8032BRVG](/sequence-files/IGVFFI8032BRVG/), [IGVFFI6392ULTE](/sequence-files/IGVFFI6392ULTE/), [IGVFFI2868ZCYM](/sequence-files/IGVFFI2868ZCYM/), [IGVFFI9747MXBT](/sequence-files/IGVFFI9747MXBT/) 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/IGVFDS2600XYHD/"
}
]
},
"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": "2024-02-29T16:49:44.574098+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/IGVFFI5245DMCW/",
"accession": "IGVFFI5245DMCW",
"aliases": [
"gary-hon:LW283C_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:23:01.498865+00:00",
"file_format": "fastq",
"file_size": 86605050,
"href": "/sequence-files/IGVFFI5245DMCW/@@download/IGVFFI5245DMCW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/650196aa-4b91-48aa-80f9-94423a0d8b21/IGVFFI5245DMCW.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/LW283C_S7_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3918UPES/",
"accession": "IGVFFI3918UPES",
"aliases": [
"gary-hon:LW283C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:22:42.626575+00:00",
"file_format": "fastq",
"file_size": 106093340,
"href": "/sequence-files/IGVFFI3918UPES/@@download/IGVFFI3918UPES.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/4ff7abe4-ee53-45f4-bafa-0d80584ffbe3/IGVFFI3918UPES.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/LW283C_S7_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7518XBAK/",
"accession": "IGVFFI7518XBAK",
"aliases": [
"gary-hon:LW283C_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:23:06.048296+00:00",
"file_format": "fastq",
"file_size": 94657295,
"href": "/sequence-files/IGVFFI7518XBAK/@@download/IGVFFI7518XBAK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/a2f37d88-8905-4774-92ef-f3d1561da28f/IGVFFI7518XBAK.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/LW283C_S7_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9972BHWI/",
"accession": "IGVFFI9972BHWI",
"aliases": [
"gary-hon:LW283C_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:23:16.674425+00:00",
"file_format": "fastq",
"file_size": 452740682,
"href": "/sequence-files/IGVFFI9972BHWI/@@download/IGVFFI9972BHWI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/9f1b633a-5f9a-4fea-b886-311d8b484bd4/IGVFFI9972BHWI.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/LW283C_S7_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8032BRVG/",
"accession": "IGVFFI8032BRVG",
"aliases": [
"gary-hon:LW283C_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:23:10.807840+00:00",
"file_format": "fastq",
"file_size": 224621955,
"href": "/sequence-files/IGVFFI8032BRVG/@@download/IGVFFI8032BRVG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/883d8360-a350-406b-8c4c-86123155ffb4/IGVFFI8032BRVG.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/LW283C_S7_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6392ULTE/",
"accession": "IGVFFI6392ULTE",
"aliases": [
"gary-hon:LW283C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:22:47.293061+00:00",
"file_format": "fastq",
"file_size": 249859211,
"href": "/sequence-files/IGVFFI6392ULTE/@@download/IGVFFI6392ULTE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/d9e9dab7-42f6-4b36-8bbd-b1f485be5f33/IGVFFI6392ULTE.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/LW283C_S7_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2868ZCYM/",
"accession": "IGVFFI2868ZCYM",
"aliases": [
"gary-hon:LW283C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:22:53.272560+00:00",
"file_format": "fastq",
"file_size": 505810367,
"href": "/sequence-files/IGVFFI2868ZCYM/@@download/IGVFFI2868ZCYM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/0d00ebc6-e370-46d9-ad8c-a582f37804ef/IGVFFI2868ZCYM.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/LW283C_S7_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9747MXBT/",
"accession": "IGVFFI9747MXBT",
"aliases": [
"gary-hon:LW283C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:22:37.789278+00:00",
"file_format": "fastq",
"file_size": 97399876,
"href": "/sequence-files/IGVFFI9747MXBT/@@download/IGVFFI9747MXBT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/bf18a3f9-8d86-4412-b476-7e2f1e77bdc4/IGVFFI9747MXBT.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/LW283C_S7_L001_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/IGVFDS4028IRAH/",
"accession": "IGVFDS4028IRAH",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW283"
],
"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/IGVFSM8464JMJS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8464JMJS",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW283"
],
"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_LW283), 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": "2024-03-01T17:22:37.789278+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": "d7f8e4b3-c2e3-4aa8-94ab-4f633b7cd291"
}