{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0882RKGQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0882RKGQ",
"aliases": [
"jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep2_bin2"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7436UMQD](/in-vitro-systems/IGVFSM7436UMQD/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/in-vitro-systems/IGVFSM7436UMQD/"
},
{
"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 sequencing kit",
"detail": "Measurement set [IGVFDS0882RKGQ](/measurement-sets/IGVFDS0882RKGQ/) has sequence file(s) [IGVFFI2403GVBV](/sequence-files/IGVFFI2403GVBV/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS0882RKGQ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0882RKGQ](/measurement-sets/IGVFDS0882RKGQ/) has sequence file(s): [IGVFFI2403GVBV](/sequence-files/IGVFFI2403GVBV/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS0882RKGQ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0882RKGQ](/measurement-sets/IGVFDS0882RKGQ/) has in progress subobject publication [2e37380f-fb50-4dbc-a7ec-e9e6532c9f99](/publications/2e37380f-fb50-4dbc-a7ec-e9e6532c9f99/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0882RKGQ/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM7436UMQD](/in-vitro-systems/IGVFSM7436UMQD/) 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/IGVFSM7436UMQD/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0882RKGQ](/measurement-sets/IGVFDS0882RKGQ/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS0882RKGQ/"
}
]
},
"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/IGVFDS7621RRLM/",
"accession": "IGVFDS7621RRLM",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI1837MRQJ/",
"accession": "IGVFFI1837MRQJ",
"content_type": "guide RNA sequences",
"status": "deleted",
"summary": "GRCh38 guide RNA sequences"
},
{
"@id": "/tabular-files/IGVFFI9333CGMN/",
"accession": "IGVFFI9333CGMN",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "GRCh38 guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting candidate cis-regulatory elements in a genomic locus"
}
],
"control_for": [],
"creation_timestamp": "2024-01-12T20:51:01.681979+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"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/IGVFFI2403GVBV/",
"accession": "IGVFFI2403GVBV",
"aliases": [
"jesse-engreitz:sequence_data_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep2_bin2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T00:44:11.003121+00:00",
"file_format": "fastq",
"file_size": 76206842,
"href": "/sequence-files/IGVFFI2403GVBV/@@download/IGVFFI2403GVBV.fastq.gz",
"md5sum": "d8fbd92224e91214ab10a105bffb7f42",
"s3_uri": "s3://igvf-files/2023/12/05/99b741e5-3e79-4052-86bc-d1b800d76976/IGVFFI2403GVBV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "/Users/ronghao/Desktop/Research/data/eRZ10_FlowFISH/TLNRD1/eRZ10_FlowFISH_fastq/T2_bin2_S24_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9053MHCS/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "CRISPR FlowFISH screen",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"publications": [
{
"@id": "/publications/2e37380f-fb50-4dbc-a7ec-e9e6532c9f99/",
"publication_identifiers": [
"PMID:38326615"
],
"status": "in progress"
}
],
"release_timestamp": "2024-02-07T19:06:56.289169+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7436UMQD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7436UMQD",
"aliases": [
"jesse-engreitz:in-vitro-system_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep2_bin2"
],
"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": "released",
"summary": "Homo sapiens (female) TeloHAEC cell line (sorting details: FACS bin for 26-50% expression of TLNRD1) modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/4b2083b4-24c1-41d8-9daa-e79299f00d6e/",
"title": "Ronghao Zhou"
},
"submitted_files_timestamp": "2023-12-05T00:44:11.003121+00:00",
"summary": "CRISPR interference FlowFISH screen sorted on the expression of TLNRD1 integrating a guide (sgRNA) library targeting candidate cis-regulatory elements in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000140406/",
"geneid": "ENSG00000140406",
"name": "talin rod domain containing 1",
"status": "released",
"symbol": "TLNRD1",
"synonyms": [
"talin rod domain containing 1",
"mesoderm development candidate 1",
"talin rod domain-containing protein 1",
"TLNRD1",
"MESDC1"
]
}
],
"uuid": "b06c1aa4-3193-40db-ac36-d15553cf8336"
}