{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8705MRYI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8705MRYI",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW234"
],
"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": "Measurement set [IGVFDS8705MRYI](/measurement-sets/IGVFDS8705MRYI/) has sequence file(s) [IGVFFI4715TBJL](/sequence-files/IGVFFI4715TBJL/), [IGVFFI4139OPTS](/sequence-files/IGVFFI4139OPTS/), [IGVFFI4712RFPX](/sequence-files/IGVFFI4712RFPX/), [IGVFFI0202YJMP](/sequence-files/IGVFFI0202YJMP/) 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/IGVFDS8705MRYI/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8705MRYI](/measurement-sets/IGVFDS8705MRYI/) has sequence file(s): [IGVFFI4715TBJL](/sequence-files/IGVFFI4715TBJL/), [IGVFFI4139OPTS](/sequence-files/IGVFFI4139OPTS/), [IGVFFI4712RFPX](/sequence-files/IGVFFI4712RFPX/), [IGVFFI0202YJMP](/sequence-files/IGVFFI0202YJMP/) 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/IGVFDS8705MRYI/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0588CNDW](/auxiliary-sets/IGVFDS0588CNDW/) has sequence file(s) [IGVFFI5260PVLB](/sequence-files/IGVFFI5260PVLB/), [IGVFFI3175IIRZ](/sequence-files/IGVFFI3175IIRZ/), [IGVFFI2983OMXA](/sequence-files/IGVFFI2983OMXA/), [IGVFFI5434BAFC](/sequence-files/IGVFFI5434BAFC/), [IGVFFI9887KSTI](/sequence-files/IGVFFI9887KSTI/), [IGVFFI1014YNGM](/sequence-files/IGVFFI1014YNGM/), [IGVFFI9069TRUT](/sequence-files/IGVFFI9069TRUT/), [IGVFFI9904QNFV](/sequence-files/IGVFFI9904QNFV/) 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/IGVFDS0588CNDW/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0588CNDW](/auxiliary-sets/IGVFDS0588CNDW/) has sequence file(s): [IGVFFI5260PVLB](/sequence-files/IGVFFI5260PVLB/), [IGVFFI3175IIRZ](/sequence-files/IGVFFI3175IIRZ/), [IGVFFI2983OMXA](/sequence-files/IGVFFI2983OMXA/), [IGVFFI5434BAFC](/sequence-files/IGVFFI5434BAFC/), [IGVFFI9887KSTI](/sequence-files/IGVFFI9887KSTI/), [IGVFFI1014YNGM](/sequence-files/IGVFFI1014YNGM/), [IGVFFI9069TRUT](/sequence-files/IGVFFI9069TRUT/), [IGVFFI9904QNFV](/sequence-files/IGVFFI9904QNFV/) 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/IGVFDS0588CNDW/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS2136RFQE](/auxiliary-sets/IGVFDS2136RFQE/) has sequence file(s) [IGVFFI5301SVVG](/sequence-files/IGVFFI5301SVVG/), [IGVFFI9083IKUZ](/sequence-files/IGVFFI9083IKUZ/), [IGVFFI8490GAUK](/sequence-files/IGVFFI8490GAUK/), [IGVFFI6705RMUI](/sequence-files/IGVFFI6705RMUI/), [IGVFFI2829XKCE](/sequence-files/IGVFFI2829XKCE/), [IGVFFI1008SZVT](/sequence-files/IGVFFI1008SZVT/), [IGVFFI0084VSYK](/sequence-files/IGVFFI0084VSYK/), [IGVFFI5975FQYH](/sequence-files/IGVFFI5975FQYH/) 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/IGVFDS2136RFQE/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2136RFQE](/auxiliary-sets/IGVFDS2136RFQE/) has sequence file(s): [IGVFFI5301SVVG](/sequence-files/IGVFFI5301SVVG/), [IGVFFI9083IKUZ](/sequence-files/IGVFFI9083IKUZ/), [IGVFFI8490GAUK](/sequence-files/IGVFFI8490GAUK/), [IGVFFI6705RMUI](/sequence-files/IGVFFI6705RMUI/), [IGVFFI2829XKCE](/sequence-files/IGVFFI2829XKCE/), [IGVFFI1008SZVT](/sequence-files/IGVFFI1008SZVT/), [IGVFFI0084VSYK](/sequence-files/IGVFFI0084VSYK/), [IGVFFI5975FQYH](/sequence-files/IGVFFI5975FQYH/) 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/IGVFDS2136RFQE/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0588CNDW/",
"accession": "IGVFDS0588CNDW",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW234"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS2136RFQE/",
"accession": "IGVFDS2136RFQE",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW234"
],
"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": "2024-02-15T23:43:15.403478+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/IGVFFI4715TBJL/",
"accession": "IGVFFI4715TBJL",
"aliases": [
"gary-hon:LW234_4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:16:46.712912+00:00",
"file_format": "fastq",
"file_size": 1971756048,
"href": "/sequence-files/IGVFFI4715TBJL/@@download/IGVFFI4715TBJL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/84da2f17-2764-416c-8a60-92c355c069bd/IGVFFI4715TBJL.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/LW234_S6_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4139OPTS/",
"accession": "IGVFFI4139OPTS",
"aliases": [
"gary-hon:LW234_4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:17:09.281261+00:00",
"file_format": "fastq",
"file_size": 2178727650,
"href": "/sequence-files/IGVFFI4139OPTS/@@download/IGVFFI4139OPTS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/78801892-b4bb-410f-9a32-60538daca8ea/IGVFFI4139OPTS.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/LW234_S6_L004_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4712RFPX/",
"accession": "IGVFFI4712RFPX",
"aliases": [
"gary-hon:LW234_4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:17:33.270932+00:00",
"file_format": "fastq",
"file_size": 27472806251,
"href": "/sequence-files/IGVFFI4712RFPX/@@download/IGVFFI4712RFPX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/4ee88f21-c827-4e33-aeb5-99b666047c1f/IGVFFI4712RFPX.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/LW234_S6_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0202YJMP/",
"accession": "IGVFFI0202YJMP",
"aliases": [
"gary-hon:LW234_4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:21:34.298752+00:00",
"file_format": "fastq",
"file_size": 26992096284,
"href": "/sequence-files/IGVFFI0202YJMP/@@download/IGVFFI0202YJMP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/fa9b489e-8d57-4fb8-bd10-20c40f3a0f25/IGVFFI0202YJMP.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/LW234_S6_L004_R2_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/IGVFSM8137TZJW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8137TZJW",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW234"
],
"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_LW264), 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": "2024-02-21T18:24:35.114092+00:00",
"submitter_comment": "Transcriptiome for LW234'",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "5723e9aa-6033-4b68-b7e8-e8c5aaacbc2c"
}