{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4629NPBV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4629NPBV",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW428"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003660/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2536BETY](/auxiliary-sets/IGVFDS2536BETY/) has sequence file(s): [IGVFFI5824TPXK](/sequence-files/IGVFFI5824TPXK/), [IGVFFI5824GVQO](/sequence-files/IGVFFI5824GVQO/), [IGVFFI9466GZAJ](/sequence-files/IGVFFI9466GZAJ/), [IGVFFI7907JKFW](/sequence-files/IGVFFI7907JKFW/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS2536BETY/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3364ARLO](/auxiliary-sets/IGVFDS3364ARLO/) has sequence file(s): [IGVFFI8532WKSQ](/sequence-files/IGVFFI8532WKSQ/), [IGVFFI4200FCBP](/sequence-files/IGVFFI4200FCBP/), [IGVFFI2569OGTA](/sequence-files/IGVFFI2569OGTA/), [IGVFFI5449YBBK](/sequence-files/IGVFFI5449YBBK/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS3364ARLO/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4629NPBV](/measurement-sets/IGVFDS4629NPBV/) has sequence file(s): [IGVFFI1376IPNG](/sequence-files/IGVFFI1376IPNG/), [IGVFFI8352DRGR](/sequence-files/IGVFFI8352DRGR/), [IGVFFI4738LNAN](/sequence-files/IGVFFI4738LNAN/), [IGVFFI4473XKFF](/sequence-files/IGVFFI4473XKFF/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS4629NPBV/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4629NPBV](/measurement-sets/IGVFDS4629NPBV/) has a sequence file [IGVFFI4738LNAN](/sequence-files/IGVFFI4738LNAN/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4629NPBV/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4629NPBV](/measurement-sets/IGVFDS4629NPBV/) has a sequence file [IGVFFI4473XKFF](/sequence-files/IGVFFI4473XKFF/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4629NPBV/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS4629NPBV](/measurement-sets/IGVFDS4629NPBV/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_strand_specificity",
"path": "/measurement-sets/IGVFDS4629NPBV/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2536BETY/",
"accession": "IGVFDS2536BETY",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_sgRNA_LW428"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3364ARLO/",
"accession": "IGVFDS3364ARLO",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_HTO_LW428"
],
"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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS0346MQBH/",
"accession": "IGVFDS0346MQBH",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI9879UTKX/",
"accession": "IGVFFI9879UTKX",
"content_type": "guide RNA sequences",
"status": "in progress",
"summary": "guide RNA sequences"
}
],
"status": "preview",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2024-08-16T20:31:54.059818+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"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/IGVFFI1376IPNG/",
"accession": "IGVFFI1376IPNG",
"aliases": [
"gary-hon:LW428_4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T21:40:17.935697+00:00",
"file_format": "fastq",
"file_size": 3660633181,
"href": "/sequence-files/IGVFFI1376IPNG/@@download/IGVFFI1376IPNG.fastq.gz",
"md5sum": "d9832c62012649be31d62cb2eb2a6699",
"s3_uri": "s3://igvf-files/2025/01/14/138843d3-fa22-418b-8ee5-dcfa55caf5d7/IGVFFI1376IPNG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon17_18/scRNA///LW428_S4_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8352DRGR/",
"accession": "IGVFFI8352DRGR",
"aliases": [
"gary-hon:LW428_4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T21:40:58.556076+00:00",
"file_format": "fastq",
"file_size": 3241330896,
"href": "/sequence-files/IGVFFI8352DRGR/@@download/IGVFFI8352DRGR.fastq.gz",
"md5sum": "33f764ab1b194f5017235c0cfcec821d",
"s3_uri": "s3://igvf-files/2025/01/14/f0f161e5-52ed-412a-9efa-5b4e98d73867/IGVFFI8352DRGR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon17_18/scRNA///LW428_S4_L004_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4738LNAN/",
"accession": "IGVFFI4738LNAN",
"aliases": [
"gary-hon:LW428_4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T21:41:36.120334+00:00",
"file_format": "fastq",
"file_size": 40209004684,
"href": "/sequence-files/IGVFFI4738LNAN/@@download/IGVFFI4738LNAN.fastq.gz",
"md5sum": "9ceb3d50cc0c6ba314ceb17141e64292",
"s3_uri": "s3://igvf-files/2025/01/14/6f4fb7c7-8da1-4e19-a187-67ebd51614c9/IGVFFI4738LNAN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon17_18/scRNA///LW428_S4_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4473XKFF/",
"accession": "IGVFFI4473XKFF",
"aliases": [
"gary-hon:LW428_4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T21:47:33.453775+00:00",
"file_format": "fastq",
"file_size": 40582669450,
"href": "/sequence-files/IGVFFI4473XKFF/@@download/IGVFFI4473XKFF.fastq.gz",
"md5sum": "a7322655aa802b9d38c9b5b2821af0ee",
"s3_uri": "s3://igvf-files/2025/01/14/83a2173c-0375-4b2d-9f6b-fd060313e378/IGVFFI4473XKFF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022841/",
"status": "released",
"term_name": "Illumina NovaSeq X Plus"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon17_18/scRNA///LW428_S4_L004_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5498SDRJ/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"onlist_files": [
"/tabular-files/IGVFFI9487JPEN/"
],
"onlist_method": "no combination",
"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/IGVFSM9285BBSI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9285BBSI",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW428"
],
"cellular_sub_pool": "subpool_LW428",
"classifications": [
"differentiated cell specimen"
],
"institutional_certificates": [],
"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": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW428) 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": "26",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2025-01-14T21:27:40.923679+00:00",
"submitter_comment": "Transcriptiome for LW428",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "b5e78c9d-4aa8-405b-a2b1-1bb79a64d525"
}