{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4323LXLZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4323LXLZ",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW233"
],
"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 sequencing kit",
"detail": "Auxiliary set [IGVFDS2333GHSM](/auxiliary-sets/IGVFDS2333GHSM/) has sequence file(s) [IGVFFI1584GGDI](/sequence-files/IGVFFI1584GGDI/), [IGVFFI2281VAEQ](/sequence-files/IGVFFI2281VAEQ/), [IGVFFI1706QJEX](/sequence-files/IGVFFI1706QJEX/), [IGVFFI5770WTCG](/sequence-files/IGVFFI5770WTCG/), [IGVFFI7279SSPT](/sequence-files/IGVFFI7279SSPT/), [IGVFFI5345XBBP](/sequence-files/IGVFFI5345XBBP/), [IGVFFI6506QHJL](/sequence-files/IGVFFI6506QHJL/), [IGVFFI4697NIDB](/sequence-files/IGVFFI4697NIDB/) 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/IGVFDS2333GHSM/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2333GHSM](/auxiliary-sets/IGVFDS2333GHSM/) has sequence file(s): [IGVFFI1584GGDI](/sequence-files/IGVFFI1584GGDI/), [IGVFFI2281VAEQ](/sequence-files/IGVFFI2281VAEQ/), [IGVFFI1706QJEX](/sequence-files/IGVFFI1706QJEX/), [IGVFFI5770WTCG](/sequence-files/IGVFFI5770WTCG/), [IGVFFI7279SSPT](/sequence-files/IGVFFI7279SSPT/), [IGVFFI5345XBBP](/sequence-files/IGVFFI5345XBBP/), [IGVFFI6506QHJL](/sequence-files/IGVFFI6506QHJL/), [IGVFFI4697NIDB](/sequence-files/IGVFFI4697NIDB/) 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/IGVFDS2333GHSM/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4323LXLZ](/measurement-sets/IGVFDS4323LXLZ/) has sequence file(s) [IGVFFI5544QVHM](/sequence-files/IGVFFI5544QVHM/), [IGVFFI3311QNGC](/sequence-files/IGVFFI3311QNGC/), [IGVFFI5292XPIK](/sequence-files/IGVFFI5292XPIK/), [IGVFFI1007NNDJ](/sequence-files/IGVFFI1007NNDJ/) 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": "/measurement-sets/IGVFDS4323LXLZ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4323LXLZ](/measurement-sets/IGVFDS4323LXLZ/) has sequence file(s): [IGVFFI5544QVHM](/sequence-files/IGVFFI5544QVHM/), [IGVFFI3311QNGC](/sequence-files/IGVFFI3311QNGC/), [IGVFFI5292XPIK](/sequence-files/IGVFFI5292XPIK/), [IGVFFI1007NNDJ](/sequence-files/IGVFFI1007NNDJ/) 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/IGVFDS4323LXLZ/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9856AQIW](/auxiliary-sets/IGVFDS9856AQIW/) has sequence file(s) [IGVFFI5551RHYT](/sequence-files/IGVFFI5551RHYT/), [IGVFFI6398GHSK](/sequence-files/IGVFFI6398GHSK/), [IGVFFI2977AAIK](/sequence-files/IGVFFI2977AAIK/), [IGVFFI0455IRKB](/sequence-files/IGVFFI0455IRKB/), [IGVFFI4423PKGT](/sequence-files/IGVFFI4423PKGT/), [IGVFFI6674LNJC](/sequence-files/IGVFFI6674LNJC/), [IGVFFI2799DOBT](/sequence-files/IGVFFI2799DOBT/), [IGVFFI6392CKYO](/sequence-files/IGVFFI6392CKYO/) 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/IGVFDS9856AQIW/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9856AQIW](/auxiliary-sets/IGVFDS9856AQIW/) has sequence file(s): [IGVFFI5551RHYT](/sequence-files/IGVFFI5551RHYT/), [IGVFFI6398GHSK](/sequence-files/IGVFFI6398GHSK/), [IGVFFI2977AAIK](/sequence-files/IGVFFI2977AAIK/), [IGVFFI0455IRKB](/sequence-files/IGVFFI0455IRKB/), [IGVFFI4423PKGT](/sequence-files/IGVFFI4423PKGT/), [IGVFFI6674LNJC](/sequence-files/IGVFFI6674LNJC/), [IGVFFI2799DOBT](/sequence-files/IGVFFI2799DOBT/), [IGVFFI6392CKYO](/sequence-files/IGVFFI6392CKYO/) 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/IGVFDS9856AQIW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9856AQIW/",
"accession": "IGVFDS9856AQIW",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW233"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS2333GHSM/",
"accession": "IGVFDS2333GHSM",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW233"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
}
],
"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"
},
"control_for": [],
"creation_timestamp": "2024-02-15T23:43:13.769083+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI5544QVHM/",
"accession": "IGVFFI5544QVHM",
"aliases": [
"gary-hon:LW233_4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:08:06.844479+00:00",
"file_format": "fastq",
"file_size": 2130477665,
"href": "/sequence-files/IGVFFI5544QVHM/@@download/IGVFFI5544QVHM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/e44c011e-9635-4b9d-91e9-dc893051eba6/IGVFFI5544QVHM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-22-McDermott-NovaSeq.10X/10X/LW233_S5_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3311QNGC/",
"accession": "IGVFFI3311QNGC",
"aliases": [
"gary-hon:LW233_4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:12:50.783616+00:00",
"file_format": "fastq",
"file_size": 26739761053,
"href": "/sequence-files/IGVFFI3311QNGC/@@download/IGVFFI3311QNGC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/c497d5aa-28f2-4a0e-9d88-c94d7e023eb6/IGVFFI3311QNGC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-22-McDermott-NovaSeq.10X/10X/LW233_S5_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5292XPIK/",
"accession": "IGVFFI5292XPIK",
"aliases": [
"gary-hon:LW233_4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:08:30.768318+00:00",
"file_format": "fastq",
"file_size": 2147089609,
"href": "/sequence-files/IGVFFI5292XPIK/@@download/IGVFFI5292XPIK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/ab47dd0a-a33b-4a58-aee9-1edb72f256dd/IGVFFI5292XPIK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-22-McDermott-NovaSeq.10X/10X/LW233_S5_L004_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1007NNDJ/",
"accession": "IGVFFI1007NNDJ",
"aliases": [
"gary-hon:LW233_4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:08:54.270065+00:00",
"file_format": "fastq",
"file_size": 27096806573,
"href": "/sequence-files/IGVFFI1007NNDJ/@@download/IGVFFI1007NNDJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/8185dd4a-3481-42dd-a886-baa4de033ae8/IGVFFI1007NNDJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-22-McDermott-NovaSeq.10X/10X/LW233_S5_L004_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9192YMGI/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"preferred_assay_title": "Perturb-seq",
"protocols": [
"https://www.protocols.io/view/experimental-procedures-for-tf-perturb-seq-ut-sout-denf3dbn"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9371INZC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9371INZC",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW233"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS9629YZLO/",
"accession": "IGVFDS9629YZLO",
"file_set_type": "guide library",
"status": "preview",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"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_LW263), 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": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-02-21T18:22:05.042900+00:00",
"submitter_comment": "Transcriptiome for LW233'",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "089942f3-ca9a-4679-b560-468c562de2af"
}