{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3876QHZN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3876QHZN",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_Lenti_LW269"
],
"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 [IGVFDS2962WEZD](/auxiliary-sets/IGVFDS2962WEZD/) has sequence file(s) [IGVFFI1432AGLB](/sequence-files/IGVFFI1432AGLB/), [IGVFFI4369QHSV](/sequence-files/IGVFFI4369QHSV/), [IGVFFI8707URKI](/sequence-files/IGVFFI8707URKI/), [IGVFFI1372GMFD](/sequence-files/IGVFFI1372GMFD/) 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/IGVFDS2962WEZD/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2962WEZD](/auxiliary-sets/IGVFDS2962WEZD/) has sequence file(s): [IGVFFI1432AGLB](/sequence-files/IGVFFI1432AGLB/), [IGVFFI4369QHSV](/sequence-files/IGVFFI4369QHSV/), [IGVFFI8707URKI](/sequence-files/IGVFFI8707URKI/), [IGVFFI1372GMFD](/sequence-files/IGVFFI1372GMFD/) 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/IGVFDS2962WEZD/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5720GLEJ](/auxiliary-sets/IGVFDS5720GLEJ/) has sequence file(s) [IGVFFI6234SPQP](/sequence-files/IGVFFI6234SPQP/), [IGVFFI1365SKHU](/sequence-files/IGVFFI1365SKHU/), [IGVFFI9167GYMH](/sequence-files/IGVFFI9167GYMH/), [IGVFFI6623ZLXQ](/sequence-files/IGVFFI6623ZLXQ/) 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/IGVFDS5720GLEJ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5720GLEJ](/auxiliary-sets/IGVFDS5720GLEJ/) has sequence file(s): [IGVFFI6234SPQP](/sequence-files/IGVFFI6234SPQP/), [IGVFFI1365SKHU](/sequence-files/IGVFFI1365SKHU/), [IGVFFI9167GYMH](/sequence-files/IGVFFI9167GYMH/), [IGVFFI6623ZLXQ](/sequence-files/IGVFFI6623ZLXQ/) 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/IGVFDS5720GLEJ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3876QHZN](/measurement-sets/IGVFDS3876QHZN/) has sequence file(s) [IGVFFI5859RWZH](/sequence-files/IGVFFI5859RWZH/), [IGVFFI2944MHGP](/sequence-files/IGVFFI2944MHGP/), [IGVFFI0273KGMQ](/sequence-files/IGVFFI0273KGMQ/), [IGVFFI4637LPPI](/sequence-files/IGVFFI4637LPPI/) 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/IGVFDS3876QHZN/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3876QHZN](/measurement-sets/IGVFDS3876QHZN/) has sequence file(s): [IGVFFI5859RWZH](/sequence-files/IGVFFI5859RWZH/), [IGVFFI2944MHGP](/sequence-files/IGVFFI2944MHGP/), [IGVFFI0273KGMQ](/sequence-files/IGVFFI0273KGMQ/), [IGVFFI4637LPPI](/sequence-files/IGVFFI4637LPPI/) 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/IGVFDS3876QHZN/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2962WEZD/",
"accession": "IGVFDS2962WEZD",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_Lenti_LW269"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS5720GLEJ/",
"accession": "IGVFDS5720GLEJ",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_HTO_Lenti_LW269"
],
"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": "2024-04-25T21:58:41.161824+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/IGVFFI5859RWZH/",
"accession": "IGVFFI5859RWZH",
"aliases": [
"gary-hon:LW269_8_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:20:40.821315+00:00",
"file_format": "fastq",
"file_size": 928508215,
"href": "/sequence-files/IGVFFI5859RWZH/@@download/IGVFFI5859RWZH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/51ff3cac-e80b-46fb-988a-4f5644358502/IGVFFI5859RWZH.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//LW269_S1_L008_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2944MHGP/",
"accession": "IGVFFI2944MHGP",
"aliases": [
"gary-hon:LW269_8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:22:41.667507+00:00",
"file_format": "fastq",
"file_size": 10558650709,
"href": "/sequence-files/IGVFFI2944MHGP/@@download/IGVFFI2944MHGP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/c16cdba7-3652-4f95-81d1-01fd8c6e9314/IGVFFI2944MHGP.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//LW269_S1_L008_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0273KGMQ/",
"accession": "IGVFFI0273KGMQ",
"aliases": [
"gary-hon:LW269_8_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:21:08.372599+00:00",
"file_format": "fastq",
"file_size": 10506870444,
"href": "/sequence-files/IGVFFI0273KGMQ/@@download/IGVFFI0273KGMQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/2ec6af41-e51a-4910-bcec-ec174e9af98c/IGVFFI0273KGMQ.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//LW269_S1_L008_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4637LPPI/",
"accession": "IGVFFI4637LPPI",
"aliases": [
"gary-hon:LW269_8_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:20:53.479146+00:00",
"file_format": "fastq",
"file_size": 1079096710,
"href": "/sequence-files/IGVFFI4637LPPI/@@download/IGVFFI4637LPPI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/60d7d2df-9ef2-4a0c-9c78-f9e0618e6d1e/IGVFFI4637LPPI.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//LW269_S1_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/IGVFSM9223FAYO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9223FAYO",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_Lenti_LW269"
],
"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_LW269), 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": "2024-04-25T22:20:40.821315+00:00",
"submitter_comment": "Transcriptiome for LW269",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "9b5317bc-e1d6-49bb-b155-1ff918037682"
}