{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS5514EBWS/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS5514EBWS",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_PB_LW274"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5514EBWS](/auxiliary-sets/IGVFDS5514EBWS/) has sequence file(s) [IGVFFI8633CSSL](/sequence-files/IGVFFI8633CSSL/), [IGVFFI4088GWUY](/sequence-files/IGVFFI4088GWUY/), [IGVFFI3088BUJP](/sequence-files/IGVFFI3088BUJP/), [IGVFFI5368RJHA](/sequence-files/IGVFFI5368RJHA/) 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/IGVFDS5514EBWS/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5514EBWS](/auxiliary-sets/IGVFDS5514EBWS/) has sequence file(s): [IGVFFI8633CSSL](/sequence-files/IGVFFI8633CSSL/), [IGVFFI4088GWUY](/sequence-files/IGVFFI4088GWUY/), [IGVFFI3088BUJP](/sequence-files/IGVFFI3088BUJP/), [IGVFFI5368RJHA](/sequence-files/IGVFFI5368RJHA/) 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/IGVFDS5514EBWS/"
}
]
},
"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": "2024-04-25T21:44:15.083148+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2718IDDQ/",
"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI8633CSSL/",
"accession": "IGVFFI8633CSSL",
"aliases": [
"gary-hon:LW274B_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:59:08.970016+00:00",
"file_format": "fastq",
"file_size": 208729422,
"href": "/sequence-files/IGVFFI8633CSSL/@@download/IGVFFI8633CSSL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/7d412585-0476-478c-afef-425501337d83/IGVFFI8633CSSL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-09-11-McDermott-NextSeq.10X/2023-09-11/outs/fastq_path/AACYY52M5//LW274B_S14_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4088GWUY/",
"accession": "IGVFFI4088GWUY",
"aliases": [
"gary-hon:LW274B_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:59:03.242854+00:00",
"file_format": "fastq",
"file_size": 194542268,
"href": "/sequence-files/IGVFFI4088GWUY/@@download/IGVFFI4088GWUY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/ef3bc00f-a653-4194-b1e9-57953ef056b3/IGVFFI4088GWUY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-09-11-McDermott-NextSeq.10X/2023-09-11/outs/fastq_path/AACYY52M5//LW274B_S14_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3088BUJP/",
"accession": "IGVFFI3088BUJP",
"aliases": [
"gary-hon:LW274B_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:59:14.514920+00:00",
"file_format": "fastq",
"file_size": 616570059,
"href": "/sequence-files/IGVFFI3088BUJP/@@download/IGVFFI3088BUJP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/7332d596-7651-4d2e-b4e0-11d8d3955052/IGVFFI3088BUJP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-09-11-McDermott-NextSeq.10X/2023-09-11/outs/fastq_path/AACYY52M5//LW274B_S14_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5368RJHA/",
"accession": "IGVFFI5368RJHA",
"aliases": [
"gary-hon:LW274B_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:59:23.538679+00:00",
"file_format": "fastq",
"file_size": 1040936154,
"href": "/sequence-files/IGVFFI5368RJHA/@@download/IGVFFI5368RJHA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/f15be076-dc07-4260-b118-a16124f45f13/IGVFFI5368RJHA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-09-11-McDermott-NextSeq.10X/2023-09-11/outs/fastq_path/AACYY52M5//LW274B_S14_L001_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4762GRIW/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0235TTEW/",
"accession": "IGVFDS0235TTEW",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_PB_LW274"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5849QIEI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5849QIEI",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_PB_LW274"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0003045/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H9"
],
"status": "released",
"summary": "H9",
"term_name": "H9"
}
],
"status": "preview",
"summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW274), female, Homo sapiens modified with CRISPRi Sp-dCas9, transfected 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": "2024-04-25T22:59:03.242854+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "3a720b54-b12f-4497-ba40-5ae5e75a66b4"
}