{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3910MZMQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3910MZMQ",
"aliases": [
"igvf:multiome_scatac_seq"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"ERROR": [
{
"category": "upload status not validated",
"detail": "Configuration file [IGVFFI1190FVNM](/configuration-files/IGVFFI1190FVNM/) has `upload_status` pending. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/configuration-files/IGVFFI1190FVNM/"
},
{
"category": "missing related files",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has seqspec configuration file [IGVFFI1190FVNM](/configuration-files/IGVFFI1190FVNM/) which links to sequence file(s): [IGVFFI4710CQYT](/sequence-files/IGVFFI4710CQYT/) which do not link to this file set. All files associated with a seqspec (both sequencing and seqspec files) are expected to be linked to the same file set.",
"level": 60,
"level_name": "ERROR",
"name": "audit_files_associated_with_incorrect_fileset",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
},
{
"category": "inconsistent preferred assay title",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has `assay_term` single-cell ATAC-seq, but `preferred_assay_title` VAMP-seq. Measurement sets are expected to specify an appropriate preferred assay title for its respective assay term.",
"level": 60,
"level_name": "ERROR",
"name": "audit_preferred_assay_title",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
},
{
"category": "unexpected multiome size",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has `multiome_size`. Only measurement sets from multiome assays are expected to specify a multiome size.",
"level": 60,
"level_name": "ERROR",
"name": "audit_related_multiome_datasets",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
},
{
"category": "inconsistent multiome datasets",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has a `multiome_size` of 2, but no `related_multiome_datasets`. Measurement sets with a multiome size are expected to have the corresponding amount of measurement sets (excluding itself) listed in related multiome datasets. Each of these datasets are expected to have the same multiome size and samples.",
"level": 60,
"level_name": "ERROR",
"name": "audit_related_multiome_datasets",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
},
{
"category": "inconsistent document type",
"detail": "Sequence file [IGVFFI2658WGRW](/sequence-files/IGVFFI2658WGRW/) has `file_format_specification` [d8ce793f-933b-45ea-9611-1c3f80cb7e11](/documents/d8ce793f-933b-45ea-9611-1c3f80cb7e11/) with `document_type` plasmid map. File format specifications are excepted to be documents have type file format specification.",
"level": 60,
"level_name": "ERROR",
"name": "audit_file_format_specifications",
"path": "/sequence-files/IGVFFI2658WGRW/"
},
{
"category": "upload status not validated",
"detail": "Sequence file [IGVFFI2658WGRW](/sequence-files/IGVFFI2658WGRW/) has `upload_status` pending. Files are expected to be validated or validation exempted.",
"level": 60,
"level_name": "ERROR",
"name": "audit_upload_status",
"path": "/sequence-files/IGVFFI2658WGRW/"
}
],
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released human donor [IGVFDO9208RPQQ](/human-donors/IGVFDO9208RPQQ/) has in progress subobject publication [59c63dd9-b5fb-4768-8045-ed8c0003a40c](/publications/59c63dd9-b5fb-4768-8045-ed8c0003a40c/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO9208RPQQ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has in progress subobject in vitro system [IGVFSM2795QSOV](/in-vitro-systems/IGVFSM2795QSOV/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing control type",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has no `control_type`. File sets that are controls for other file sets are expected to define a control type.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_control_for_control_type",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has sequence file(s) [IGVFFI2658WGRW](/sequence-files/IGVFFI2658WGRW/), [IGVFFI9343YZPC](/sequence-files/IGVFFI9343YZPC/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih single cell data should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has sequence file(s): [IGVFFI2658WGRW](/sequence-files/IGVFFI2658WGRW/) 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": "/measurement-sets/IGVFDS3910MZMQ/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has a sequence file [IGVFFI2658WGRW](/sequence-files/IGVFFI2658WGRW/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
},
{
"category": "missing NIH certification",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has a sample [IGVFSM2795QSOV](/in-vitro-systems/IGVFSM2795QSOV/) that lacks any `institutional_certificates` issued to the lab that submitted this file set or to a partner lab/award of the submitting lab. Measurement sets for mapping assays or controlled access characterization assays involving samples with a human origin are expected to link to the relevant institutional certificates.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_institutional_certification",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_strand_specificity",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has an `assay_term` of single-cell ATAC-seq but no `onlist_files` nor `onlist_methods`. Measurement sets to be processed via the single cell uniform pipeline are expected to have onlist files and onlist methods indicated.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_onlist",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
},
{
"category": "missing protocol",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) has no `protocols`. Measurement sets are expected to specify the experimental protocol utilized for conducting the assay on protocols.io.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_unspecified_protocol",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM2795QSOV](/in-vitro-systems/IGVFSM2795QSOV/) 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/IGVFSM2795QSOV/"
},
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS3910MZMQ](/measurement-sets/IGVFDS3910MZMQ/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_for",
"path": "/measurement-sets/IGVFDS3910MZMQ/"
}
]
},
"award": {
"@id": "/awards/HG012051/",
"component": "networks",
"contact_pi": {
"@id": "/users/7138e67a-2af5-4a48-90bc-04ea95b53c78/",
"title": "Danwei Huangfu"
},
"title": "Genomic control of gene regulatory networks governing early human lineage decisions"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS0948BMCL/",
"accession": "IGVFDS0948BMCL",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/reference-files/IGVFFI4139LADO/",
"accession": "IGVFFI4139LADO",
"content_type": "genome reference",
"status": "in progress",
"summary": "genome reference"
}
],
"status": "in progress",
"summary": "guide (sgRNA) library targeting TF binding sites, phenotype-associated variants genome-wide associated with DiGeorge syndrome"
}
],
"control_for": [
{
"@id": "/measurement-sets/IGVFDS5330YIDV/",
"accession": "IGVFDS5330YIDV",
"aliases": [
"igvf:basic_measurement_set"
],
"status": "in progress"
}
],
"creation_timestamp": "2023-04-27T18:51:25.198759+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"accession": "IGVFDO9208RPQQ",
"aliases": [
"igvf:donor_of_K562"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI2658WGRW/",
"accession": "IGVFFI2658WGRW",
"aliases": [
"igvf:example_fastq_01",
"jay-shendure:example_fastq_01_alt_alias"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-05-23T20:29:58.899328+00:00",
"file_format": "fastq",
"file_size": 9898933494,
"href": "/sequence-files/IGVFFI2658WGRW/@@download/IGVFFI2658WGRW.fastq.gz",
"s3_uri": "s3://igvf-files-dev/2023/05/23/21cc5af6-5c36-4913-af85-440b4b61f383/IGVFFI2658WGRW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0004203/",
"status": "in progress",
"term_name": "Illumina HiSeq 2000"
},
"status": "in progress",
"submitted_file_name": "/path/to/sequence_file.fastq.gz",
"upload_status": "pending"
},
{
"@id": "/configuration-files/IGVFFI1190FVNM/",
"accession": "IGVFFI1190FVNM",
"aliases": [
"igvf:example_configuration_file_01"
],
"content_type": "seqspec",
"creation_timestamp": "2023-09-19T20:11:56.580713+00:00",
"file_format": "yaml",
"file_size": 1240000,
"href": "/configuration-files/IGVFFI1190FVNM/@@download/IGVFFI1190FVNM.yaml.gz",
"s3_uri": "s3://igvf-files-dev/2023/09/19/718d7475-e11b-4a1f-bdfa-899abf6c711f/IGVFFI1190FVNM.yaml",
"status": "in progress",
"submitted_file_name": "/path/to/seqspec.yaml",
"upload_status": "pending"
},
{
"@id": "/sequence-files/IGVFFI9343YZPC/",
"accession": "IGVFFI9343YZPC",
"content_type": "PacBio subreads",
"controlled_access": false,
"creation_timestamp": "2023-05-08T17:16:55.623037+00:00",
"file_format": "bam",
"file_size": 235234435,
"href": "/sequence-files/IGVFFI9343YZPC/@@download/IGVFFI9343YZPC.bam",
"s3_uri": "s3://igvf-files-dev/2023/05/08/29b7f066-9d13-4663-8fe2-cd6847ec9c5c/IGVFFI9343YZPC.bam",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0004203/",
"status": "in progress",
"term_name": "Illumina HiSeq 2000"
},
"status": "in progress",
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/danwei-huangfu/",
"title": "Danwei Huangfu, MSKCC"
},
"multiome_size": 2,
"preferred_assay_title": "VAMP-seq",
"related_multiome_datasets": [],
"release_timestamp": "2023-04-27T18:51:25.181642+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2795QSOV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2795QSOV",
"classifications": [
"cell line"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:K562"
],
"status": "released",
"summary": "K562",
"term_name": "K562"
}
],
"status": "in progress",
"summary": "Homo sapiens (female) K562 cell line transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/1e75d989-a438-4d77-a451-8a297fd3636e/",
"title": "Ian Whaling"
},
"submitted_files_timestamp": "2023-05-08T17:16:55.623037+00:00",
"summary": "CRISPR VAMP-seq integrating a guide (sgRNA) library targeting TF binding sites, phenotype-associated variants genome-wide associated with DiGeorge syndrome",
"uuid": "5663d0c7-faee-4c10-8ef5-c827fd74ad28"
}