{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS8139DLEM/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8139DLEM",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_sgRNA_LW278"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8139DLEM](/auxiliary-sets/IGVFDS8139DLEM/) has sequence file(s) [IGVFFI7706SWGW](/sequence-files/IGVFFI7706SWGW/), [IGVFFI7788FDIR](/sequence-files/IGVFFI7788FDIR/), [IGVFFI6246XEYZ](/sequence-files/IGVFFI6246XEYZ/), [IGVFFI5269EMSE](/sequence-files/IGVFFI5269EMSE/), [IGVFFI7446JOPR](/sequence-files/IGVFFI7446JOPR/), [IGVFFI2624RMQV](/sequence-files/IGVFFI2624RMQV/), [IGVFFI7302FRGV](/sequence-files/IGVFFI7302FRGV/), [IGVFFI3447MKLI](/sequence-files/IGVFFI3447MKLI/) 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/IGVFDS8139DLEM/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8139DLEM](/auxiliary-sets/IGVFDS8139DLEM/) has sequence file(s): [IGVFFI7706SWGW](/sequence-files/IGVFFI7706SWGW/), [IGVFFI7788FDIR](/sequence-files/IGVFFI7788FDIR/), [IGVFFI6246XEYZ](/sequence-files/IGVFFI6246XEYZ/), [IGVFFI5269EMSE](/sequence-files/IGVFFI5269EMSE/), [IGVFFI7446JOPR](/sequence-files/IGVFFI7446JOPR/), [IGVFFI2624RMQV](/sequence-files/IGVFFI2624RMQV/), [IGVFFI7302FRGV](/sequence-files/IGVFFI7302FRGV/), [IGVFFI3447MKLI](/sequence-files/IGVFFI3447MKLI/) 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/IGVFDS8139DLEM/"
}
]
},
"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": "2024-02-21T21:01:48.412023+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/IGVFFI7706SWGW/",
"accession": "IGVFFI7706SWGW",
"aliases": [
"gary-hon:LW278B-3_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:08:43.304651+00:00",
"file_format": "fastq",
"file_size": 580314516,
"href": "/sequence-files/IGVFFI7706SWGW/@@download/IGVFFI7706SWGW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/e5d08042-b8d9-4be3-871b-fb25c9bd03e2/IGVFFI7706SWGW.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/LW278B-3_S24_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7788FDIR/",
"accession": "IGVFFI7788FDIR",
"aliases": [
"gary-hon:LW278B-3_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:08:52.159262+00:00",
"file_format": "fastq",
"file_size": 630228841,
"href": "/sequence-files/IGVFFI7788FDIR/@@download/IGVFFI7788FDIR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/be25301d-6afd-43f4-adfa-b5ce7c446eae/IGVFFI7788FDIR.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/LW278B-3_S24_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6246XEYZ/",
"accession": "IGVFFI6246XEYZ",
"aliases": [
"gary-hon:LW278B-3_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:09:20.799153+00:00",
"file_format": "fastq",
"file_size": 574678015,
"href": "/sequence-files/IGVFFI6246XEYZ/@@download/IGVFFI6246XEYZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/c6ce3539-4393-41c7-bbec-87f49ff961bc/IGVFFI6246XEYZ.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/LW278B-3_S24_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5269EMSE/",
"accession": "IGVFFI5269EMSE",
"aliases": [
"gary-hon:LW278B-3_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:09:06.775410+00:00",
"file_format": "fastq",
"file_size": 207456689,
"href": "/sequence-files/IGVFFI5269EMSE/@@download/IGVFFI5269EMSE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/0a263f96-3fbf-42a0-814e-7f93799e17c3/IGVFFI5269EMSE.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/LW278B-3_S24_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7446JOPR/",
"accession": "IGVFFI7446JOPR",
"aliases": [
"gary-hon:LW278B-3_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:08:31.895509+00:00",
"file_format": "fastq",
"file_size": 195839455,
"href": "/sequence-files/IGVFFI7446JOPR/@@download/IGVFFI7446JOPR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/0fce6be8-4a52-4417-9134-b7e92fd0ac4d/IGVFFI7446JOPR.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/LW278B-3_S24_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2624RMQV/",
"accession": "IGVFFI2624RMQV",
"aliases": [
"gary-hon:LW278B-3_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:08:37.700912+00:00",
"file_format": "fastq",
"file_size": 222350922,
"href": "/sequence-files/IGVFFI2624RMQV/@@download/IGVFFI2624RMQV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/5c9879c0-ef14-4fca-9232-90a41dace3d5/IGVFFI2624RMQV.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/LW278B-3_S24_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7302FRGV/",
"accession": "IGVFFI7302FRGV",
"aliases": [
"gary-hon:LW278B-3_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:09:01.403130+00:00",
"file_format": "fastq",
"file_size": 179755260,
"href": "/sequence-files/IGVFFI7302FRGV/@@download/IGVFFI7302FRGV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/649c23cd-a36e-44a4-a61e-777a50c6118f/IGVFFI7302FRGV.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/LW278B-3_S24_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3447MKLI/",
"accession": "IGVFFI3447MKLI",
"aliases": [
"gary-hon:LW278B-3_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:09:12.409472+00:00",
"file_format": "fastq",
"file_size": 534665331,
"href": "/sequence-files/IGVFFI3447MKLI/@@download/IGVFFI3447MKLI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/c5d51ae4-a104-4df3-9cdb-cf4e1f86eb23/IGVFFI3447MKLI.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/LW278B-3_S24_L002_R1_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/IGVFDS2628PYOH/",
"accession": "IGVFDS2628PYOH",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_LW278"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7499ZWUW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7499ZWUW",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti_LW278"
],
"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_LW278), 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": "2024-03-01T17:08:31.895509+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "d547dfd8-2d52-47a7-bc83-38be17a0311c"
}