{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0385ESBQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0385ESBQ",
"aliases": [
"jesse-engreitz:measurement_set-scRNAseq_2kG_2PMDox1_6"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003660/",
"status": "released",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0385ESBQ](/measurement-sets/IGVFDS0385ESBQ/) has sequence file(s): [IGVFFI9790VMAE](/sequence-files/IGVFFI9790VMAE/), [IGVFFI0226LNBE](/sequence-files/IGVFFI0226LNBE/), [IGVFFI4899TNXF](/sequence-files/IGVFFI4899TNXF/) 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": "/measurement-sets/IGVFDS0385ESBQ/"
},
{
"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/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2031LFEN](/auxiliary-sets/IGVFDS2031LFEN/) has sequence file(s): [IGVFFI8535CSXL](/sequence-files/IGVFFI8535CSXL/), [IGVFFI4014XSAK](/sequence-files/IGVFFI4014XSAK/), [IGVFFI3955WSPN](/sequence-files/IGVFFI3955WSPN/), [IGVFFI6132PXBN](/sequence-files/IGVFFI6132PXBN/), [IGVFFI5712MZTB](/sequence-files/IGVFFI5712MZTB/), [IGVFFI6559SZAD](/sequence-files/IGVFFI6559SZAD/), [IGVFFI8066GKDM](/sequence-files/IGVFFI8066GKDM/), [IGVFFI0864MICP](/sequence-files/IGVFFI0864MICP/) 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/IGVFDS2031LFEN/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2031LFEN/",
"accession": "IGVFDS2031LFEN",
"aliases": [
"jesse-engreitz:auxiliary_sets-scRNAseq_2kG_2PMDox1_6"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
}
],
"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": "2024-01-18T03:10:04.363202+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO3459DFTW/",
"accession": "IGVFDO3459DFTW",
"aliases": [
"igvf:donor_of_teloHAEC"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI9790VMAE/",
"accession": "IGVFFI9790VMAE",
"aliases": [
"jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq1-scRNAseq_2kG_2PMDox1_6_S1_L001_I1_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-20T23:32:50.626102+00:00",
"file_format": "fastq",
"file_size": 3044834888,
"href": "/sequence-files/IGVFFI9790VMAE/@@download/IGVFFI9790VMAE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/20/4582b17d-c9aa-453a-b8e1-fc13d1a99b57/IGVFFI9790VMAE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/oak/stanford/groups/engreitz/Users/kangh/TeloHAEC_Perturb-seq_2kG/210528_Broad_fastq/scRNAseq_2kG_2PMDox1_6_S1_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0226LNBE/",
"accession": "IGVFFI0226LNBE",
"aliases": [
"jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq1-scRNAseq_2kG_2PMDox1_6_S1_L001_R1_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-20T23:33:24.982322+00:00",
"file_format": "fastq",
"file_size": 10638894903,
"href": "/sequence-files/IGVFFI0226LNBE/@@download/IGVFFI0226LNBE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/20/715b701f-cac7-4445-aacd-00b8c71778d0/IGVFFI0226LNBE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/oak/stanford/groups/engreitz/Users/kangh/TeloHAEC_Perturb-seq_2kG/210528_Broad_fastq/scRNAseq_2kG_2PMDox1_6_S1_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4899TNXF/",
"accession": "IGVFFI4899TNXF",
"aliases": [
"jesse-engreitz:sequence_file-teloHAEC_2kG_library-NovaSeq1-scRNAseq_2kG_2PMDox1_6_S1_L001_R2_001.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-20T23:34:58.911520+00:00",
"file_format": "fastq",
"file_size": 14285208928,
"href": "/sequence-files/IGVFFI4899TNXF/@@download/IGVFFI4899TNXF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/20/2eaa3093-d945-42e9-bbd4-3b683bc3f0b2/IGVFFI4899TNXF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/seq/landerlabCE/Users/Helen/TeloHAEC_Perturb-seq_2kG/240210_IGVF_recombined_fastqs/scRNAseq_2kG_2PMDox1_6_L001_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7943IIWZ/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 86015c12-b9a6-43ba-9601-5d75aab4d39c was removed from this measurement set.",
"preferred_assay_title": "Perturb-seq",
"protocols": [
"https://www.protocols.io/view/systematic-perturb-seq-to-discover-endothelial-cel-261ged73yv47/v1"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9019CRXH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9019CRXH",
"aliases": [
"jesse-engreitz:in_vitro_systems-scRNAseq_2kG_2PMDox1_6"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS1298TUYG/",
"accession": "IGVFDS1298TUYG",
"file_set_type": "guide library",
"status": "preview",
"summary": "guide (sgRNA) library targeting genes in many genomic loci"
}
],
"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": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/05fa0dc9-0e33-427c-9d1f-82393edc4a03/",
"title": "Helen Kang"
},
"submitted_files_timestamp": "2023-12-20T23:32:50.626102+00:00",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting genes in many genomic loci",
"uuid": "ed99fd09-9ae3-48b3-8eeb-84908cf5f1e1"
}