{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4940ELQK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4940ELQK",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_Lenti_LW272"
],
"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 [IGVFDS8839RSIR](/auxiliary-sets/IGVFDS8839RSIR/) has sequence file(s) [IGVFFI3688WTIX](/sequence-files/IGVFFI3688WTIX/), [IGVFFI0982WORL](/sequence-files/IGVFFI0982WORL/), [IGVFFI9175HBPO](/sequence-files/IGVFFI9175HBPO/), [IGVFFI8689DYXM](/sequence-files/IGVFFI8689DYXM/) 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/IGVFDS8839RSIR/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8839RSIR](/auxiliary-sets/IGVFDS8839RSIR/) has sequence file(s): [IGVFFI3688WTIX](/sequence-files/IGVFFI3688WTIX/), [IGVFFI0982WORL](/sequence-files/IGVFFI0982WORL/), [IGVFFI9175HBPO](/sequence-files/IGVFFI9175HBPO/), [IGVFFI8689DYXM](/sequence-files/IGVFFI8689DYXM/) 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/IGVFDS8839RSIR/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4940ELQK](/measurement-sets/IGVFDS4940ELQK/) has sequence file(s) [IGVFFI9431GCYS](/sequence-files/IGVFFI9431GCYS/), [IGVFFI9849UOCQ](/sequence-files/IGVFFI9849UOCQ/), [IGVFFI3780QGTX](/sequence-files/IGVFFI3780QGTX/), [IGVFFI5596FJTD](/sequence-files/IGVFFI5596FJTD/) 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/IGVFDS4940ELQK/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4940ELQK](/measurement-sets/IGVFDS4940ELQK/) has sequence file(s): [IGVFFI9431GCYS](/sequence-files/IGVFFI9431GCYS/), [IGVFFI9849UOCQ](/sequence-files/IGVFFI9849UOCQ/), [IGVFFI3780QGTX](/sequence-files/IGVFFI3780QGTX/), [IGVFFI5596FJTD](/sequence-files/IGVFFI5596FJTD/) 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/IGVFDS4940ELQK/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8726ORVQ](/auxiliary-sets/IGVFDS8726ORVQ/) has sequence file(s) [IGVFFI9255ZWLL](/sequence-files/IGVFFI9255ZWLL/), [IGVFFI9316DTIE](/sequence-files/IGVFFI9316DTIE/), [IGVFFI0045RQHO](/sequence-files/IGVFFI0045RQHO/), [IGVFFI8537ABID](/sequence-files/IGVFFI8537ABID/) 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/IGVFDS8726ORVQ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8726ORVQ](/auxiliary-sets/IGVFDS8726ORVQ/) has sequence file(s): [IGVFFI9255ZWLL](/sequence-files/IGVFFI9255ZWLL/), [IGVFFI9316DTIE](/sequence-files/IGVFFI9316DTIE/), [IGVFFI0045RQHO](/sequence-files/IGVFFI0045RQHO/), [IGVFFI8537ABID](/sequence-files/IGVFFI8537ABID/) 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/IGVFDS8726ORVQ/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8726ORVQ/",
"accession": "IGVFDS8726ORVQ",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_Lenti_LW272"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS8839RSIR/",
"accession": "IGVFDS8839RSIR",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_HTO_Lenti_LW272"
],
"file_set_type": "cell hashing barcode 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": "2024-04-25T21:58:44.556894+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2718IDDQ/",
"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI9431GCYS/",
"accession": "IGVFFI9431GCYS",
"aliases": [
"gary-hon:LW272_8_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:32:05.459034+00:00",
"file_format": "fastq",
"file_size": 10744168192,
"href": "/sequence-files/IGVFFI9431GCYS/@@download/IGVFFI9431GCYS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/676a7e46-c861-471c-8af4-1cb124e61f66/IGVFFI9431GCYS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-25-McDermott-NovaSeq.lane8.10X/10X//LW272_S4_L008_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9849UOCQ/",
"accession": "IGVFFI9849UOCQ",
"aliases": [
"gary-hon:LW272_8_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:31:41.435010+00:00",
"file_format": "fastq",
"file_size": 889063652,
"href": "/sequence-files/IGVFFI9849UOCQ/@@download/IGVFFI9849UOCQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/d3a9aa1b-8b4e-4580-b64f-1aa3a691883c/IGVFFI9849UOCQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-25-McDermott-NovaSeq.lane8.10X/10X//LW272_S4_L008_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3780QGTX/",
"accession": "IGVFFI3780QGTX",
"aliases": [
"gary-hon:LW272_8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:33:40.548950+00:00",
"file_format": "fastq",
"file_size": 10712159102,
"href": "/sequence-files/IGVFFI3780QGTX/@@download/IGVFFI3780QGTX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/d2e152f9-470f-4da0-b8a0-09e04a91c94f/IGVFFI3780QGTX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-25-McDermott-NovaSeq.lane8.10X/10X//LW272_S4_L008_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5596FJTD/",
"accession": "IGVFFI5596FJTD",
"aliases": [
"gary-hon:LW272_8_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:31:53.164601+00:00",
"file_format": "fastq",
"file_size": 962108499,
"href": "/sequence-files/IGVFFI5596FJTD/@@download/IGVFFI5596FJTD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/a6528dbe-ed27-4546-8ab5-86fa4e3c51d1/IGVFFI5596FJTD.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-25-McDermott-NovaSeq.lane8.10X/10X//LW272_S4_L008_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2873EPIU/"
],
"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/IGVFSM1608DJBB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1608DJBB",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_Lenti_LW272"
],
"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_0003045/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H9"
],
"status": "released",
"summary": "H9",
"term_name": "H9"
}
],
"status": "preview",
"summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW272), female, 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": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-04-25T22:31:41.435010+00:00",
"submitter_comment": "Transcriptiome for LW272",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "b3693b1f-c89a-4184-8c00-652813a7fdf4"
}