{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5228AHGR/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5228AHGR",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_HTO_LW280"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5228AHGR](/auxiliary-sets/IGVFDS5228AHGR/) has sequence file(s) [IGVFFI3880AUGY](/sequence-files/IGVFFI3880AUGY/), [IGVFFI3453EWPB](/sequence-files/IGVFFI3453EWPB/), [IGVFFI0680SUCW](/sequence-files/IGVFFI0680SUCW/), [IGVFFI1694KFBX](/sequence-files/IGVFFI1694KFBX/), [IGVFFI3489PXOT](/sequence-files/IGVFFI3489PXOT/), [IGVFFI5218TWQD](/sequence-files/IGVFFI5218TWQD/), [IGVFFI2754LNUW](/sequence-files/IGVFFI2754LNUW/), [IGVFFI3423UPCF](/sequence-files/IGVFFI3423UPCF/) 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/IGVFDS5228AHGR/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5228AHGR](/auxiliary-sets/IGVFDS5228AHGR/) has sequence file(s): [IGVFFI3880AUGY](/sequence-files/IGVFFI3880AUGY/), [IGVFFI3453EWPB](/sequence-files/IGVFFI3453EWPB/), [IGVFFI0680SUCW](/sequence-files/IGVFFI0680SUCW/), [IGVFFI1694KFBX](/sequence-files/IGVFFI1694KFBX/), [IGVFFI3489PXOT](/sequence-files/IGVFFI3489PXOT/), [IGVFFI5218TWQD](/sequence-files/IGVFFI5218TWQD/), [IGVFFI2754LNUW](/sequence-files/IGVFFI2754LNUW/), [IGVFFI3423UPCF](/sequence-files/IGVFFI3423UPCF/) 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/IGVFDS5228AHGR/"
}
]
},
"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": "2024-02-21T21:01:55.755302+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/IGVFFI3880AUGY/",
"accession": "IGVFFI3880AUGY",
"aliases": [
"gary-hon:LW280C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:14:55.414611+00:00",
"file_format": "fastq",
"file_size": 252326981,
"href": "/sequence-files/IGVFFI3880AUGY/@@download/IGVFFI3880AUGY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/559f2655-e912-4ecf-ab95-44a90e1e83ff/IGVFFI3880AUGY.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/LW280C_S4_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3453EWPB/",
"accession": "IGVFFI3453EWPB",
"aliases": [
"gary-hon:LW280C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:15:01.314061+00:00",
"file_format": "fastq",
"file_size": 491288453,
"href": "/sequence-files/IGVFFI3453EWPB/@@download/IGVFFI3453EWPB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/3afd7528-5310-4f21-89c5-7fc47555d224/IGVFFI3453EWPB.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/LW280C_S4_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0680SUCW/",
"accession": "IGVFFI0680SUCW",
"aliases": [
"gary-hon:LW280C_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:15:09.358977+00:00",
"file_format": "fastq",
"file_size": 77620563,
"href": "/sequence-files/IGVFFI0680SUCW/@@download/IGVFFI0680SUCW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/5fd20646-983f-40ed-aa29-6ca2f39b20bd/IGVFFI0680SUCW.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/LW280C_S4_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1694KFBX/",
"accession": "IGVFFI1694KFBX",
"aliases": [
"gary-hon:LW280C_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:15:13.758583+00:00",
"file_format": "fastq",
"file_size": 73503752,
"href": "/sequence-files/IGVFFI1694KFBX/@@download/IGVFFI1694KFBX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/4b567c49-edf5-4796-88d8-49f71dde6431/IGVFFI1694KFBX.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/LW280C_S4_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3489PXOT/",
"accession": "IGVFFI3489PXOT",
"aliases": [
"gary-hon:LW280C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:14:46.390988+00:00",
"file_format": "fastq",
"file_size": 84175795,
"href": "/sequence-files/IGVFFI3489PXOT/@@download/IGVFFI3489PXOT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/7f7c124c-97e3-4e6f-8af4-5bba86ccfacc/IGVFFI3489PXOT.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/LW280C_S4_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5218TWQD/",
"accession": "IGVFFI5218TWQD",
"aliases": [
"gary-hon:LW280C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:14:50.853183+00:00",
"file_format": "fastq",
"file_size": 86244472,
"href": "/sequence-files/IGVFFI5218TWQD/@@download/IGVFFI5218TWQD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/13a4cf58-1d26-413e-b20c-81a85ae05453/IGVFFI5218TWQD.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/LW280C_S4_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2754LNUW/",
"accession": "IGVFFI2754LNUW",
"aliases": [
"gary-hon:LW280C_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:15:18.183254+00:00",
"file_format": "fastq",
"file_size": 225834466,
"href": "/sequence-files/IGVFFI2754LNUW/@@download/IGVFFI2754LNUW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/608f00d2-40fc-4601-aef1-d943b90b6d2d/IGVFFI2754LNUW.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/LW280C_S4_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3423UPCF/",
"accession": "IGVFFI3423UPCF",
"aliases": [
"gary-hon:LW280C_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:15:24.173073+00:00",
"file_format": "fastq",
"file_size": 437788295,
"href": "/sequence-files/IGVFFI3423UPCF/@@download/IGVFFI3423UPCF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/035b3f35-27c0-4241-98ca-e090d7d4dbed/IGVFFI3423UPCF.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/LW280C_S4_L002_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4389OUWU/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS4852MAUM/",
"accession": "IGVFDS4852MAUM",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_LW280"
],
"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/IGVFSM0604KDJF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0604KDJF",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti_LW280"
],
"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 cardiac muscle cell for 12 days (cellular sub pool: subpool_LW280), 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": "2024-03-01T17:14:46.390988+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": "d29fc73e-0404-4e61-93de-3aa963334996"
}