{
"@context": "/terms/",
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"AuxiliarySet",
"FileSet",
"Item"
],
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"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_sgRNA_LW279"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0997MTQA](/auxiliary-sets/IGVFDS0997MTQA/) has sequence file(s) [IGVFFI5758JYDL](/sequence-files/IGVFFI5758JYDL/), [IGVFFI0808FCCO](/sequence-files/IGVFFI0808FCCO/), [IGVFFI7852BFOU](/sequence-files/IGVFFI7852BFOU/), [IGVFFI3938OJKT](/sequence-files/IGVFFI3938OJKT/), [IGVFFI9797JSJB](/sequence-files/IGVFFI9797JSJB/), [IGVFFI2834JYDA](/sequence-files/IGVFFI2834JYDA/), [IGVFFI7620POLB](/sequence-files/IGVFFI7620POLB/), [IGVFFI4290KTZN](/sequence-files/IGVFFI4290KTZN/) 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/IGVFDS0997MTQA/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0997MTQA](/auxiliary-sets/IGVFDS0997MTQA/) has sequence file(s): [IGVFFI5758JYDL](/sequence-files/IGVFFI5758JYDL/), [IGVFFI0808FCCO](/sequence-files/IGVFFI0808FCCO/), [IGVFFI7852BFOU](/sequence-files/IGVFFI7852BFOU/), [IGVFFI3938OJKT](/sequence-files/IGVFFI3938OJKT/), [IGVFFI9797JSJB](/sequence-files/IGVFFI9797JSJB/), [IGVFFI2834JYDA](/sequence-files/IGVFFI2834JYDA/), [IGVFFI7620POLB](/sequence-files/IGVFFI7620POLB/), [IGVFFI4290KTZN](/sequence-files/IGVFFI4290KTZN/) 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/IGVFDS0997MTQA/"
}
]
},
"award": {
"@id": "/awards/HG011996/",
"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": "2024-02-21T21:01:50.759246+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": "2024-03-01T17:11:11.419344+00:00",
"file_format": "fastq",
"file_size": 216775264,
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"status": "preview",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0808FCCO/",
"accession": "IGVFFI0808FCCO",
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:11:46.602381+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI0808FCCO/@@download/IGVFFI0808FCCO.fastq.gz",
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"status": "preview",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7852BFOU/",
"accession": "IGVFFI7852BFOU",
"aliases": [
"gary-hon:LW279B-3_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:11:55.358224+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI7852BFOU/@@download/IGVFFI7852BFOU.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW279B-3_S25_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3938OJKT/",
"accession": "IGVFFI3938OJKT",
"aliases": [
"gary-hon:LW279B-3_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:11:06.130701+00:00",
"file_format": "fastq",
"file_size": 194560427,
"href": "/sequence-files/IGVFFI3938OJKT/@@download/IGVFFI3938OJKT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/aa9765e1-02a1-4dda-adfe-bf1f4f197516/IGVFFI3938OJKT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW279B-3_S25_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9797JSJB/",
"accession": "IGVFFI9797JSJB",
"aliases": [
"gary-hon:LW279B-3_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:11:17.189681+00:00",
"file_format": "fastq",
"file_size": 621448352,
"href": "/sequence-files/IGVFFI9797JSJB/@@download/IGVFFI9797JSJB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/e06fe53a-ea56-4419-b8ec-f7ae0ec78bb3/IGVFFI9797JSJB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW279B-3_S25_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2834JYDA/",
"accession": "IGVFFI2834JYDA",
"aliases": [
"gary-hon:LW279B-3_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:11:26.198007+00:00",
"file_format": "fastq",
"file_size": 670029663,
"href": "/sequence-files/IGVFFI2834JYDA/@@download/IGVFFI2834JYDA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/38cd5e8f-6528-4c3b-ae3f-1cf0afc94edd/IGVFFI2834JYDA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW279B-3_S25_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7620POLB/",
"accession": "IGVFFI7620POLB",
"aliases": [
"gary-hon:LW279B-3_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:11:35.856062+00:00",
"file_format": "fastq",
"file_size": 179244420,
"href": "/sequence-files/IGVFFI7620POLB/@@download/IGVFFI7620POLB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/d1c89619-d1b0-4d3e-ad41-902dcae4d34f/IGVFFI7620POLB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW279B-3_S25_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4290KTZN/",
"accession": "IGVFFI4290KTZN",
"aliases": [
"gary-hon:LW279B-3_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:11:41.177285+00:00",
"file_format": "fastq",
"file_size": 194748424,
"href": "/sequence-files/IGVFFI4290KTZN/@@download/IGVFFI4290KTZN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/e2261e90-2618-4e15-89b2-f532304d35d2/IGVFFI4290KTZN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW279B-3_S25_L002_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4389OUWU/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS7733OTCA/",
"accession": "IGVFDS7733OTCA",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_LW279"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0559UNMK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0559UNMK",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti_LW279"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS2302LCEO/"
],
"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_LW279), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) 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": "2024-03-01T17:11:06.130701+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "af2acaa2-b27d-4126-b2b2-653e1197cdf1"
}