{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5158EDZB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5158EDZB",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_Lenti_LW270"
],
"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 [IGVFDS6931FVDN](/auxiliary-sets/IGVFDS6931FVDN/) has sequence file(s) [IGVFFI2394RQHG](/sequence-files/IGVFFI2394RQHG/), [IGVFFI4585UXOH](/sequence-files/IGVFFI4585UXOH/), [IGVFFI6540PTZG](/sequence-files/IGVFFI6540PTZG/), [IGVFFI5552GLZY](/sequence-files/IGVFFI5552GLZY/) 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/IGVFDS6931FVDN/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6931FVDN](/auxiliary-sets/IGVFDS6931FVDN/) has sequence file(s): [IGVFFI2394RQHG](/sequence-files/IGVFFI2394RQHG/), [IGVFFI4585UXOH](/sequence-files/IGVFFI4585UXOH/), [IGVFFI6540PTZG](/sequence-files/IGVFFI6540PTZG/), [IGVFFI5552GLZY](/sequence-files/IGVFFI5552GLZY/) 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/IGVFDS6931FVDN/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5158EDZB](/measurement-sets/IGVFDS5158EDZB/) has sequence file(s) [IGVFFI5952WLSN](/sequence-files/IGVFFI5952WLSN/), [IGVFFI1626FQFD](/sequence-files/IGVFFI1626FQFD/), [IGVFFI2748IVWJ](/sequence-files/IGVFFI2748IVWJ/), [IGVFFI4775VFYE](/sequence-files/IGVFFI4775VFYE/) 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/IGVFDS5158EDZB/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5158EDZB](/measurement-sets/IGVFDS5158EDZB/) has sequence file(s): [IGVFFI5952WLSN](/sequence-files/IGVFFI5952WLSN/), [IGVFFI1626FQFD](/sequence-files/IGVFFI1626FQFD/), [IGVFFI2748IVWJ](/sequence-files/IGVFFI2748IVWJ/), [IGVFFI4775VFYE](/sequence-files/IGVFFI4775VFYE/) 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/IGVFDS5158EDZB/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8999BYPM](/auxiliary-sets/IGVFDS8999BYPM/) has sequence file(s) [IGVFFI1806DNML](/sequence-files/IGVFFI1806DNML/), [IGVFFI4609VMSG](/sequence-files/IGVFFI4609VMSG/), [IGVFFI1585MDUT](/sequence-files/IGVFFI1585MDUT/), [IGVFFI6112XIWA](/sequence-files/IGVFFI6112XIWA/) 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/IGVFDS8999BYPM/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8999BYPM](/auxiliary-sets/IGVFDS8999BYPM/) has sequence file(s): [IGVFFI1806DNML](/sequence-files/IGVFFI1806DNML/), [IGVFFI4609VMSG](/sequence-files/IGVFFI4609VMSG/), [IGVFFI1585MDUT](/sequence-files/IGVFFI1585MDUT/), [IGVFFI6112XIWA](/sequence-files/IGVFFI6112XIWA/) 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/IGVFDS8999BYPM/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6931FVDN/",
"accession": "IGVFDS6931FVDN",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_Lenti_LW270"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS8999BYPM/",
"accession": "IGVFDS8999BYPM",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_HTO_Lenti_LW270"
],
"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": "2024-04-25T21:58:42.226403+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/IGVFFI5952WLSN/",
"accession": "IGVFFI5952WLSN",
"aliases": [
"gary-hon:LW270_8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:26:19.815489+00:00",
"file_format": "fastq",
"file_size": 11073099356,
"href": "/sequence-files/IGVFFI5952WLSN/@@download/IGVFFI5952WLSN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/5a31b706-f3a3-43cd-b7e9-6972208ca002/IGVFFI5952WLSN.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//LW270_S2_L008_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1626FQFD/",
"accession": "IGVFFI1626FQFD",
"aliases": [
"gary-hon:LW270_8_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:24:30.289611+00:00",
"file_format": "fastq",
"file_size": 854163830,
"href": "/sequence-files/IGVFFI1626FQFD/@@download/IGVFFI1626FQFD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/40d7a141-a0c9-439e-973f-cf265a54083c/IGVFFI1626FQFD.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//LW270_S2_L008_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2748IVWJ/",
"accession": "IGVFFI2748IVWJ",
"aliases": [
"gary-hon:LW270_8_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:24:42.478312+00:00",
"file_format": "fastq",
"file_size": 10958234818,
"href": "/sequence-files/IGVFFI2748IVWJ/@@download/IGVFFI2748IVWJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/ee7188f3-f830-484d-aadf-581e0e316bc2/IGVFFI2748IVWJ.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//LW270_S2_L008_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4775VFYE/",
"accession": "IGVFFI4775VFYE",
"aliases": [
"gary-hon:LW270_8_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:24:17.587974+00:00",
"file_format": "fastq",
"file_size": 978560203,
"href": "/sequence-files/IGVFFI4775VFYE/@@download/IGVFFI4775VFYE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/af6a6f0e-d218-4644-9ee3-518a35ced55b/IGVFFI4775VFYE.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//LW270_S2_L008_I1_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/IGVFSM6628JOOL/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6628JOOL",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_Lenti_LW270"
],
"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_LW270), 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": "2024-04-25T22:24:17.587974+00:00",
"submitter_comment": "Transcriptiome for LW270",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "9b625dfd-516d-4bb3-b74d-06c4e52ae265"
}