{
"@context": "/terms/",
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"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS0616JFOF",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox1_5"
],
"audit": {
"INTERNAL_ACTION": [
{
"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/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0616JFOF](/auxiliary-sets/IGVFDS0616JFOF/) has sequence file(s): [IGVFFI4920MOQE](/sequence-files/IGVFFI4920MOQE/), [IGVFFI0354EWAS](/sequence-files/IGVFFI0354EWAS/), [IGVFFI9851LYSX](/sequence-files/IGVFFI9851LYSX/), [IGVFFI1114ENMU](/sequence-files/IGVFFI1114ENMU/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS0616JFOF/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM1061NWCP](/in-vitro-systems/IGVFSM1061NWCP/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM1061NWCP/"
}
]
},
"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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS1298TUYG/",
"accession": "IGVFDS1298TUYG",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI9754AGFB/",
"accession": "IGVFFI9754AGFB",
"content_type": "guide RNA sequences",
"status": "in progress",
"summary": "GRCh38 guide RNA sequences"
}
],
"status": "preview",
"summary": "guide (sgRNA) library targeting genes in many genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2024-02-06T19:29:39.680257+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/IGVFFI4920MOQE/",
"accession": "IGVFFI4920MOQE",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:22:03.006386+00:00",
"file_format": "fastq",
"file_size": 434677387,
"href": "/sequence-files/IGVFFI4920MOQE/@@download/IGVFFI4920MOQE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/50335df5-5f10-4edf-86bf-742187300492/IGVFFI4920MOQE.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_2PMDox1_5.2_CGTTACCA_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0354EWAS/",
"accession": "IGVFFI0354EWAS",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox1_5_redo_CGTTACCA_L001_R2_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:21:57.644128+00:00",
"file_format": "fastq",
"file_size": 289061073,
"href": "/sequence-files/IGVFFI0354EWAS/@@download/IGVFFI0354EWAS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/61a7999a-22d2-4f0e-842d-997763b699f9/IGVFFI0354EWAS.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_2PMDox1_5_redo_CGTTACCA_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9851LYSX/",
"accession": "IGVFFI9851LYSX",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox1_5.2_CGTTACCA_L001_R2_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:22:13.031584+00:00",
"file_format": "fastq",
"file_size": 420480969,
"href": "/sequence-files/IGVFFI9851LYSX/@@download/IGVFFI9851LYSX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/b817442b-c889-47aa-81ad-abb403080bdb/IGVFFI9851LYSX.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_2PMDox1_5.2_CGTTACCA_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1114ENMU/",
"accession": "IGVFFI1114ENMU",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox1_5_redo_CGTTACCA_L001_R1_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:21:52.917047+00:00",
"file_format": "fastq",
"file_size": 248636242,
"href": "/sequence-files/IGVFFI1114ENMU/@@download/IGVFFI1114ENMU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/31073122-79fa-4433-9389-ac44921a7d72/IGVFFI1114ENMU.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_2PMDox1_5_redo_CGTTACCA_L001_R1_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/IGVFDS0237AFZT/",
"accession": "IGVFDS0237AFZT",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox1_5"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1061NWCP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1061NWCP",
"aliases": [
"jesse-engreitz:in_vitro_systems-scRNAseq_2kG_2PMDox1_5"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"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": "Homo sapiens (female) TeloHAEC cell line 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": "2024-02-06T21:21:52.917047+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting genes in many genomic loci",
"uuid": "12f454ae-2cea-42a0-a7bf-3901bc4db99f"
}