{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS8509JBZW/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8509JBZW",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox2_7"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8509JBZW](/auxiliary-sets/IGVFDS8509JBZW/) has sequence file(s): [IGVFFI4169AJLD](/sequence-files/IGVFFI4169AJLD/), [IGVFFI8014NHMB](/sequence-files/IGVFFI8014NHMB/), [IGVFFI3861DNWW](/sequence-files/IGVFFI3861DNWW/), [IGVFFI3085EGKA](/sequence-files/IGVFFI3085EGKA/) 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/IGVFDS8509JBZW/"
},
{
"category": "NTR term ID",
"detail": "Sample term for [NTR_0000753](/sample-terms/NTR_0000753/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
"path": "/sample-terms/NTR_0000753/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_for": [],
"creation_timestamp": "2024-02-06T19:29:47.906483+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO3459DFTW/",
"accession": "IGVFDO3459DFTW",
"aliases": [
"igvf:donor_of_teloHAEC"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI4169AJLD/",
"accession": "IGVFFI4169AJLD",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox2_7_GGTCCAGA_L001_R2_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:26:45.540994+00:00",
"file_format": "fastq",
"file_size": 535102285,
"href": "/sequence-files/IGVFFI4169AJLD/@@download/IGVFFI4169AJLD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/2dbfd215-9cab-41f6-af73-c39b9ab27bd9/IGVFFI4169AJLD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0009173/",
"status": "preview",
"submitted_file_name": "/oak/stanford/groups/engreitz/Users/gschnitz/dialout_files_for_helen/Dialout_2kg_2PMDox2_7_GGTCCAGA_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8014NHMB/",
"accession": "IGVFFI8014NHMB",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox2_7.2_GGTCCAGA_L001_R1_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:26:53.044475+00:00",
"file_format": "fastq",
"file_size": 500761538,
"href": "/sequence-files/IGVFFI8014NHMB/@@download/IGVFFI8014NHMB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/3841126b-d760-400f-92fd-9300c215e078/IGVFFI8014NHMB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0009173/",
"status": "preview",
"submitted_file_name": "/oak/stanford/groups/engreitz/Users/gschnitz/dialout_files_for_helen/Dialout_2kg_2PMDox2_7.2_GGTCCAGA_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3861DNWW/",
"accession": "IGVFFI3861DNWW",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox2_7_GGTCCAGA_L001_R1_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:26:38.642101+00:00",
"file_format": "fastq",
"file_size": 461887259,
"href": "/sequence-files/IGVFFI3861DNWW/@@download/IGVFFI3861DNWW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/70b779b8-cea8-4479-b67c-a00187e7cdbe/IGVFFI3861DNWW.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0009173/",
"status": "preview",
"submitted_file_name": "/oak/stanford/groups/engreitz/Users/gschnitz/dialout_files_for_helen/Dialout_2kg_2PMDox2_7_GGTCCAGA_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3085EGKA/",
"accession": "IGVFFI3085EGKA",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox2_7.2_GGTCCAGA_L001_R2_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:27:00.775808+00:00",
"file_format": "fastq",
"file_size": 484308604,
"href": "/sequence-files/IGVFFI3085EGKA/@@download/IGVFFI3085EGKA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/4347c7a9-c6c8-4f81-8980-d2d8a2f372b8/IGVFFI3085EGKA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0009173/",
"status": "preview",
"submitted_file_name": "/oak/stanford/groups/engreitz/Users/gschnitz/dialout_files_for_helen/Dialout_2kg_2PMDox2_7.2_GGTCCAGA_L001_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7943IIWZ/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0909ARVL/",
"accession": "IGVFDS0909ARVL",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox2_7"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9362CZWG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9362CZWG",
"aliases": [
"jesse-engreitz:in_vitro_systems-scRNAseq_2kG_2PMDox2_7"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS1298TUYG/"
],
"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000753/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:TeloHAEC"
],
"status": "released",
"summary": "TeloHAEC",
"term_name": "TeloHAEC"
}
],
"status": "preview",
"summary": "TeloHAEC cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "preview",
"submitted_by": {
"@id": "/users/4b2083b4-24c1-41d8-9daa-e79299f00d6e/",
"title": "Ronghao Zhou"
},
"submitted_files_timestamp": "2024-02-06T21:26:38.642101+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting genes in many genomic loci",
"uuid": "c5592b1a-fbb8-460f-8342-9262ac121cab"
}