{
"@context": "/terms/",
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"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
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"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox2_1"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4784DDTU](/auxiliary-sets/IGVFDS4784DDTU/) has sequence file(s): [IGVFFI4092GRZQ](/sequence-files/IGVFFI4092GRZQ/), [IGVFFI1378RGUV](/sequence-files/IGVFFI1378RGUV/), [IGVFFI7575DTDH](/sequence-files/IGVFFI7575DTDH/), [IGVFFI4619DNJG](/sequence-files/IGVFFI4619DNJG/) 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/IGVFDS4784DDTU/"
},
{
"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": "2024-02-06T19:29:42.627674+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",
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{
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"accession": "IGVFFI4092GRZQ",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox2_1_ACAGGTAT_L001_R2_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:23:52.857241+00:00",
"file_format": "fastq",
"file_size": 537848328,
"href": "/sequence-files/IGVFFI4092GRZQ/@@download/IGVFFI4092GRZQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/de18552c-f1cf-49ce-bf02-ccfe385676b0/IGVFFI4092GRZQ.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_1_ACAGGTAT_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1378RGUV/",
"accession": "IGVFFI1378RGUV",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox2_1_ACAGGTAT_L001_R1_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:23:45.891366+00:00",
"file_format": "fastq",
"file_size": 464624201,
"href": "/sequence-files/IGVFFI1378RGUV/@@download/IGVFFI1378RGUV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/f30320b5-1a55-47c8-8af0-985ba96714e0/IGVFFI1378RGUV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0009173/",
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"submitted_file_name": "/oak/stanford/groups/engreitz/Users/gschnitz/dialout_files_for_helen/Dialout_2kg_2PMDox2_1_ACAGGTAT_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7575DTDH/",
"accession": "IGVFFI7575DTDH",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox2_1.2_ACAGGTAT_L001_R2_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:24:09.719206+00:00",
"file_format": "fastq",
"file_size": 673919330,
"href": "/sequence-files/IGVFFI7575DTDH/@@download/IGVFFI7575DTDH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/3a9843fa-7b6d-4dcd-87a1-b330ce7078fa/IGVFFI7575DTDH.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_1.2_ACAGGTAT_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4619DNJG/",
"accession": "IGVFFI4619DNJG",
"aliases": [
"jesse-engreitz:sequence_files-TeloHAEC_Perturb-seq_2kG-Dialout_2kg_2PMDox2_1.2_ACAGGTAT_L001_R1_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-06T21:24:00.877131+00:00",
"file_format": "fastq",
"file_size": 704180815,
"href": "/sequence-files/IGVFFI4619DNJG/@@download/IGVFFI4619DNJG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/06/32c57b9f-3612-49a0-81ac-fddb2bc89d5c/IGVFFI4619DNJG.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_1.2_ACAGGTAT_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/IGVFDS7600PZYR/",
"accession": "IGVFDS7600PZYR",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox2_1"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0862BZMH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0862BZMH",
"aliases": [
"jesse-engreitz:in_vitro_systems-scRNAseq_2kG_2PMDox2_1"
],
"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": "2024-02-06T21:23:45.891366+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting genes in many genomic loci",
"uuid": "4da44b26-21c1-4da2-a93d-020d297d7f72"
}