{
"@context": "/terms/",
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"AuxiliarySet",
"FileSet",
"Item"
],
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"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW235"
],
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"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7242KAVQ](/auxiliary-sets/IGVFDS7242KAVQ/) has sequence file(s) [IGVFFI9103HDFO](/sequence-files/IGVFFI9103HDFO/), [IGVFFI8160QLNB](/sequence-files/IGVFFI8160QLNB/), [IGVFFI6722SNGU](/sequence-files/IGVFFI6722SNGU/), [IGVFFI4482FUJT](/sequence-files/IGVFFI4482FUJT/), [IGVFFI1066MCTM](/sequence-files/IGVFFI1066MCTM/), [IGVFFI5213ROQB](/sequence-files/IGVFFI5213ROQB/), [IGVFFI5528NTNB](/sequence-files/IGVFFI5528NTNB/), [IGVFFI8013NSZD](/sequence-files/IGVFFI8013NSZD/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS7242KAVQ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7242KAVQ](/auxiliary-sets/IGVFDS7242KAVQ/) has sequence file(s): [IGVFFI9103HDFO](/sequence-files/IGVFFI9103HDFO/), [IGVFFI8160QLNB](/sequence-files/IGVFFI8160QLNB/), [IGVFFI6722SNGU](/sequence-files/IGVFFI6722SNGU/), [IGVFFI4482FUJT](/sequence-files/IGVFFI4482FUJT/), [IGVFFI1066MCTM](/sequence-files/IGVFFI1066MCTM/), [IGVFFI5213ROQB](/sequence-files/IGVFFI5213ROQB/), [IGVFFI5528NTNB](/sequence-files/IGVFFI5528NTNB/), [IGVFFI8013NSZD](/sequence-files/IGVFFI8013NSZD/) 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/IGVFDS7242KAVQ/"
}
]
},
"award": {
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"component": "functional characterization",
"contact_pi": {
"@id": "/users/95d84f03-8ce0-489c-a755-f33ced139c5d/",
"title": "Gary Hon"
},
"title": "Multiscale functional characterization of genomic variation in human developmental disorders"
},
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"creation_timestamp": "2024-02-15T23:35:41.257671+00:00",
"donors": [
{
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"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
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{
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"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:27:18.346729+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI9103HDFO/@@download/IGVFFI9103HDFO.fastq.gz",
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"status": "preview",
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"upload_status": "validated"
},
{
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"accession": "IGVFFI8160QLNB",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:27:51.566720+00:00",
"file_format": "fastq",
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"sequencing_platform": "/platform-terms/EFO_0010963/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6722SNGU/",
"accession": "IGVFFI6722SNGU",
"aliases": [
"gary-hon:LW235B-2_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:27:58.082284+00:00",
"file_format": "fastq",
"file_size": 279231491,
"href": "/sequence-files/IGVFFI6722SNGU/@@download/IGVFFI6722SNGU.fastq.gz",
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"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW235B-2_S5_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4482FUJT/",
"accession": "IGVFFI4482FUJT",
"aliases": [
"gary-hon:LW235B-2_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:27:11.745382+00:00",
"file_format": "fastq",
"file_size": 295508812,
"href": "/sequence-files/IGVFFI4482FUJT/@@download/IGVFFI4482FUJT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/8152753c-340b-4813-bed0-69dbc071f6e5/IGVFFI4482FUJT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW235B-2_S5_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1066MCTM/",
"accession": "IGVFFI1066MCTM",
"aliases": [
"gary-hon:LW235B-2_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:28:04.579352+00:00",
"file_format": "fastq",
"file_size": 1056709309,
"href": "/sequence-files/IGVFFI1066MCTM/@@download/IGVFFI1066MCTM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/429e5af9-0241-41cc-80ac-ad6078598764/IGVFFI1066MCTM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW235B-2_S5_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5213ROQB/",
"accession": "IGVFFI5213ROQB",
"aliases": [
"gary-hon:LW235B-2_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:28:18.261451+00:00",
"file_format": "fastq",
"file_size": 1373813318,
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"s3_uri": "s3://igvf-files/2024/02/21/185ace20-c965-4dab-9f20-75b6f8d755e6/IGVFFI5213ROQB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW235B-2_S5_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5528NTNB/",
"accession": "IGVFFI5528NTNB",
"aliases": [
"gary-hon:LW235B-2_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:27:05.090264+00:00",
"file_format": "fastq",
"file_size": 285404360,
"href": "/sequence-files/IGVFFI5528NTNB/@@download/IGVFFI5528NTNB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/1290beef-c220-4a48-8e2c-f926299f7faf/IGVFFI5528NTNB.fastq.gz",
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"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW235B-2_S5_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8013NSZD/",
"accession": "IGVFFI8013NSZD",
"aliases": [
"gary-hon:LW235B-2_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:27:32.213140+00:00",
"file_format": "fastq",
"file_size": 1462572196,
"href": "/sequence-files/IGVFFI8013NSZD/@@download/IGVFFI8013NSZD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/967cb6d0-611c-407d-8c42-a26a4d9aee13/IGVFFI8013NSZD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW235B-2_S5_L001_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9192YMGI/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1663ZHVE/",
"accession": "IGVFDS1663ZHVE",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW235"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2930BIPX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2930BIPX",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW235"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW265), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-02-21T18:27:05.090264+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "3bb2b5b1-42bd-481d-9a30-07e3980e194e"
}