{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0890CUXC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0890CUXC",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW236"
],
"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 [IGVFDS9925GTMC](/auxiliary-sets/IGVFDS9925GTMC/) has sequence file(s) [IGVFFI7364IONS](/sequence-files/IGVFFI7364IONS/), [IGVFFI7549VRUY](/sequence-files/IGVFFI7549VRUY/), [IGVFFI9116NYPQ](/sequence-files/IGVFFI9116NYPQ/), [IGVFFI5839AQOX](/sequence-files/IGVFFI5839AQOX/), [IGVFFI5160RFGF](/sequence-files/IGVFFI5160RFGF/), [IGVFFI7687IOMO](/sequence-files/IGVFFI7687IOMO/), [IGVFFI5328JRCC](/sequence-files/IGVFFI5328JRCC/), [IGVFFI3400AXGE](/sequence-files/IGVFFI3400AXGE/) 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/IGVFDS9925GTMC/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9925GTMC](/auxiliary-sets/IGVFDS9925GTMC/) has sequence file(s): [IGVFFI7364IONS](/sequence-files/IGVFFI7364IONS/), [IGVFFI7549VRUY](/sequence-files/IGVFFI7549VRUY/), [IGVFFI9116NYPQ](/sequence-files/IGVFFI9116NYPQ/), [IGVFFI5839AQOX](/sequence-files/IGVFFI5839AQOX/), [IGVFFI5160RFGF](/sequence-files/IGVFFI5160RFGF/), [IGVFFI7687IOMO](/sequence-files/IGVFFI7687IOMO/), [IGVFFI5328JRCC](/sequence-files/IGVFFI5328JRCC/), [IGVFFI3400AXGE](/sequence-files/IGVFFI3400AXGE/) 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/IGVFDS9925GTMC/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9976WMCI](/auxiliary-sets/IGVFDS9976WMCI/) has sequence file(s) [IGVFFI3939YRKP](/sequence-files/IGVFFI3939YRKP/), [IGVFFI8413FBXY](/sequence-files/IGVFFI8413FBXY/), [IGVFFI7863LXLL](/sequence-files/IGVFFI7863LXLL/), [IGVFFI1976BTXC](/sequence-files/IGVFFI1976BTXC/), [IGVFFI8279OHEK](/sequence-files/IGVFFI8279OHEK/), [IGVFFI1480DNXC](/sequence-files/IGVFFI1480DNXC/), [IGVFFI8928YFKN](/sequence-files/IGVFFI8928YFKN/), [IGVFFI8077IAPC](/sequence-files/IGVFFI8077IAPC/) 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/IGVFDS9976WMCI/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9976WMCI](/auxiliary-sets/IGVFDS9976WMCI/) has sequence file(s): [IGVFFI3939YRKP](/sequence-files/IGVFFI3939YRKP/), [IGVFFI8413FBXY](/sequence-files/IGVFFI8413FBXY/), [IGVFFI7863LXLL](/sequence-files/IGVFFI7863LXLL/), [IGVFFI1976BTXC](/sequence-files/IGVFFI1976BTXC/), [IGVFFI8279OHEK](/sequence-files/IGVFFI8279OHEK/), [IGVFFI1480DNXC](/sequence-files/IGVFFI1480DNXC/), [IGVFFI8928YFKN](/sequence-files/IGVFFI8928YFKN/), [IGVFFI8077IAPC](/sequence-files/IGVFFI8077IAPC/) 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/IGVFDS9976WMCI/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0890CUXC](/measurement-sets/IGVFDS0890CUXC/) has sequence file(s) [IGVFFI8488QBKR](/sequence-files/IGVFFI8488QBKR/), [IGVFFI6938RERD](/sequence-files/IGVFFI6938RERD/), [IGVFFI1162EYEZ](/sequence-files/IGVFFI1162EYEZ/), [IGVFFI7270YUBH](/sequence-files/IGVFFI7270YUBH/) 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/IGVFDS0890CUXC/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0890CUXC](/measurement-sets/IGVFDS0890CUXC/) has sequence file(s): [IGVFFI8488QBKR](/sequence-files/IGVFFI8488QBKR/), [IGVFFI6938RERD](/sequence-files/IGVFFI6938RERD/), [IGVFFI1162EYEZ](/sequence-files/IGVFFI1162EYEZ/), [IGVFFI7270YUBH](/sequence-files/IGVFFI7270YUBH/) 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/IGVFDS0890CUXC/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9925GTMC/",
"accession": "IGVFDS9925GTMC",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW236"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS9976WMCI/",
"accession": "IGVFDS9976WMCI",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW236"
],
"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": "2024-02-15T23:43:17.636405+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/IGVFFI8488QBKR/",
"accession": "IGVFFI8488QBKR",
"aliases": [
"gary-hon:LW236_4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:33:08.198958+00:00",
"file_format": "fastq",
"file_size": 1904167080,
"href": "/sequence-files/IGVFFI8488QBKR/@@download/IGVFFI8488QBKR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/46b43450-8045-4dfc-9889-25920e7e35b0/IGVFFI8488QBKR.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/LW236_S8_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6938RERD/",
"accession": "IGVFFI6938RERD",
"aliases": [
"gary-hon:LW236_4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:33:30.253897+00:00",
"file_format": "fastq",
"file_size": 2058521464,
"href": "/sequence-files/IGVFFI6938RERD/@@download/IGVFFI6938RERD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/badb768d-4f29-4171-80a3-5ded0e4b0621/IGVFFI6938RERD.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/LW236_S8_L004_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1162EYEZ/",
"accession": "IGVFFI1162EYEZ",
"aliases": [
"gary-hon:LW236_4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:33:53.095661+00:00",
"file_format": "fastq",
"file_size": 24611295872,
"href": "/sequence-files/IGVFFI1162EYEZ/@@download/IGVFFI1162EYEZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/47262709-59ac-4cc7-b73e-1e3af8cdf25e/IGVFFI1162EYEZ.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/LW236_S8_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7270YUBH/",
"accession": "IGVFFI7270YUBH",
"aliases": [
"gary-hon:LW236_4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:37:32.058516+00:00",
"file_format": "fastq",
"file_size": 24084874236,
"href": "/sequence-files/IGVFFI7270YUBH/@@download/IGVFFI7270YUBH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/dbc80541-67ea-4ba6-8c9d-3d734660e605/IGVFFI7270YUBH.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/LW236_S8_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/IGVFSM5652SBGF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5652SBGF",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW236"
],
"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_LW266), 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": "2024-02-21T18:29:34.337512+00:00",
"submitter_comment": "Transcriptiome for LW236'",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "495264c8-2fa3-4ec3-969a-a0415401171e"
}