{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1663ZHVE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1663ZHVE",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW235"
],
"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 [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/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1726RJYG](/auxiliary-sets/IGVFDS1726RJYG/) has sequence file(s) [IGVFFI7079PLNF](/sequence-files/IGVFFI7079PLNF/), [IGVFFI2341UENO](/sequence-files/IGVFFI2341UENO/), [IGVFFI8384IQXK](/sequence-files/IGVFFI8384IQXK/), [IGVFFI1205FYWX](/sequence-files/IGVFFI1205FYWX/), [IGVFFI3013ZQOT](/sequence-files/IGVFFI3013ZQOT/), [IGVFFI8956XELZ](/sequence-files/IGVFFI8956XELZ/), [IGVFFI5494FVJF](/sequence-files/IGVFFI5494FVJF/), [IGVFFI3707CIKC](/sequence-files/IGVFFI3707CIKC/) 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/IGVFDS1726RJYG/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1726RJYG](/auxiliary-sets/IGVFDS1726RJYG/) has sequence file(s): [IGVFFI7079PLNF](/sequence-files/IGVFFI7079PLNF/), [IGVFFI2341UENO](/sequence-files/IGVFFI2341UENO/), [IGVFFI8384IQXK](/sequence-files/IGVFFI8384IQXK/), [IGVFFI1205FYWX](/sequence-files/IGVFFI1205FYWX/), [IGVFFI3013ZQOT](/sequence-files/IGVFFI3013ZQOT/), [IGVFFI8956XELZ](/sequence-files/IGVFFI8956XELZ/), [IGVFFI5494FVJF](/sequence-files/IGVFFI5494FVJF/), [IGVFFI3707CIKC](/sequence-files/IGVFFI3707CIKC/) 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/IGVFDS1726RJYG/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1663ZHVE](/measurement-sets/IGVFDS1663ZHVE/) has sequence file(s) [IGVFFI7666WRPD](/sequence-files/IGVFFI7666WRPD/), [IGVFFI3681PXDF](/sequence-files/IGVFFI3681PXDF/), [IGVFFI8028YCLK](/sequence-files/IGVFFI8028YCLK/), [IGVFFI7462VNHZ](/sequence-files/IGVFFI7462VNHZ/) 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/IGVFDS1663ZHVE/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1663ZHVE](/measurement-sets/IGVFDS1663ZHVE/) has sequence file(s): [IGVFFI7666WRPD](/sequence-files/IGVFFI7666WRPD/), [IGVFFI3681PXDF](/sequence-files/IGVFFI3681PXDF/), [IGVFFI8028YCLK](/sequence-files/IGVFFI8028YCLK/), [IGVFFI7462VNHZ](/sequence-files/IGVFFI7462VNHZ/) 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/IGVFDS1663ZHVE/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1726RJYG/",
"accession": "IGVFDS1726RJYG",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW235"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7242KAVQ/",
"accession": "IGVFDS7242KAVQ",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW235"
],
"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": "2024-02-15T23:43:16.591171+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/IGVFFI7666WRPD/",
"accession": "IGVFFI7666WRPD",
"aliases": [
"gary-hon:LW235_4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:25:31.049643+00:00",
"file_format": "fastq",
"file_size": 1833221949,
"href": "/sequence-files/IGVFFI7666WRPD/@@download/IGVFFI7666WRPD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/1a682374-5be4-40d2-89b1-6911b337c349/IGVFFI7666WRPD.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/LW235_S7_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3681PXDF/",
"accession": "IGVFFI3681PXDF",
"aliases": [
"gary-hon:LW235_4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:25:51.972324+00:00",
"file_format": "fastq",
"file_size": 2143905814,
"href": "/sequence-files/IGVFFI3681PXDF/@@download/IGVFFI3681PXDF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/f46d221d-49d2-4812-86d6-391713418010/IGVFFI3681PXDF.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/LW235_S7_L004_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8028YCLK/",
"accession": "IGVFFI8028YCLK",
"aliases": [
"gary-hon:LW235_4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:29:42.507750+00:00",
"file_format": "fastq",
"file_size": 23467289493,
"href": "/sequence-files/IGVFFI8028YCLK/@@download/IGVFFI8028YCLK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/2e18fd18-b77a-47a8-8126-cdf3c3bc7906/IGVFFI8028YCLK.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/LW235_S7_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7462VNHZ/",
"accession": "IGVFFI7462VNHZ",
"aliases": [
"gary-hon:LW235_4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:26:15.365812+00:00",
"file_format": "fastq",
"file_size": 23709002992,
"href": "/sequence-files/IGVFFI7462VNHZ/@@download/IGVFFI7462VNHZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/1255aab9-423e-4dfb-9630-c6aaf8dfbfc7/IGVFFI7462VNHZ.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/LW235_S7_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/IGVFSM2930BIPX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2930BIPX",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW235"
],
"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_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": "23",
"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",
"submitter_comment": "Transcriptiome for LW235'",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "00b2dc30-5dd2-43d3-8051-4133a9c52ced"
}