{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3695BOGD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3695BOGD",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW429"
],
"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 [IGVFDS4210TUPX](/auxiliary-sets/IGVFDS4210TUPX/) has sequence file(s): [IGVFFI6877UQHQ](/sequence-files/IGVFFI6877UQHQ/), [IGVFFI8174NAEK](/sequence-files/IGVFFI8174NAEK/), [IGVFFI8554AKFO](/sequence-files/IGVFFI8554AKFO/), [IGVFFI2887DIIX](/sequence-files/IGVFFI2887DIIX/) 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/IGVFDS4210TUPX/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3695BOGD](/measurement-sets/IGVFDS3695BOGD/) has sequence file(s): [IGVFFI4745BDUL](/sequence-files/IGVFFI4745BDUL/), [IGVFFI0531LECP](/sequence-files/IGVFFI0531LECP/), [IGVFFI1104FBFA](/sequence-files/IGVFFI1104FBFA/), [IGVFFI7411BWKR](/sequence-files/IGVFFI7411BWKR/) 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/IGVFDS3695BOGD/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS3695BOGD](/measurement-sets/IGVFDS3695BOGD/) has a sequence file [IGVFFI4745BDUL](/sequence-files/IGVFFI4745BDUL/) 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/IGVFDS3695BOGD/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS3695BOGD](/measurement-sets/IGVFDS3695BOGD/) has a sequence file [IGVFFI7411BWKR](/sequence-files/IGVFFI7411BWKR/) 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/IGVFDS3695BOGD/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS3695BOGD](/measurement-sets/IGVFDS3695BOGD/) is missing required `strand_specificity`. Gene expression based assays are expected to specify strand specificity.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_strand_specificity",
"path": "/measurement-sets/IGVFDS3695BOGD/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4935NKQB](/auxiliary-sets/IGVFDS4935NKQB/) has sequence file(s): [IGVFFI4402LQGT](/sequence-files/IGVFFI4402LQGT/), [IGVFFI4297RVGB](/sequence-files/IGVFFI4297RVGB/), [IGVFFI8799UTTR](/sequence-files/IGVFFI8799UTTR/), [IGVFFI8421YAUU](/sequence-files/IGVFFI8421YAUU/) 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/IGVFDS4935NKQB/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4935NKQB/",
"accession": "IGVFDS4935NKQB",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_sgRNA_LW429"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS4210TUPX/",
"accession": "IGVFDS4210TUPX",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_HTO_LW429"
],
"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": "2024-08-16T20:31:56.014069+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/IGVFFI4745BDUL/",
"accession": "IGVFFI4745BDUL",
"aliases": [
"gary-hon:LW429_4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T22:00:51.351261+00:00",
"file_format": "fastq",
"file_size": 42299969993,
"href": "/sequence-files/IGVFFI4745BDUL/@@download/IGVFFI4745BDUL.fastq.gz",
"md5sum": "d57d96fde578e9684f2cff8a5bfeba39",
"s3_uri": "s3://igvf-files/2025/01/14/c1dbed0c-b2f9-4f99-9e1c-10ad25735e1c/IGVFFI4745BDUL.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///LW429_S5_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0531LECP/",
"accession": "IGVFFI0531LECP",
"aliases": [
"gary-hon:LW429_4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T21:53:28.916693+00:00",
"file_format": "fastq",
"file_size": 3262215356,
"href": "/sequence-files/IGVFFI0531LECP/@@download/IGVFFI0531LECP.fastq.gz",
"md5sum": "746e3363ab751646ccf33b3f2e7579f6",
"s3_uri": "s3://igvf-files/2025/01/14/c906cf01-4f4a-4798-98af-474171187c51/IGVFFI0531LECP.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///LW429_S5_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1104FBFA/",
"accession": "IGVFFI1104FBFA",
"aliases": [
"gary-hon:LW429_4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T21:54:04.743933+00:00",
"file_format": "fastq",
"file_size": 3307695179,
"href": "/sequence-files/IGVFFI1104FBFA/@@download/IGVFFI1104FBFA.fastq.gz",
"md5sum": "b0bd8407502e4e36a11ac86d2f81ee32",
"s3_uri": "s3://igvf-files/2025/01/14/19d55f85-5167-434a-961a-56371ba6d5b0/IGVFFI1104FBFA.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///LW429_S5_L004_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7411BWKR/",
"accession": "IGVFFI7411BWKR",
"aliases": [
"gary-hon:LW429_4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T21:54:42.634181+00:00",
"file_format": "fastq",
"file_size": 41765562572,
"href": "/sequence-files/IGVFFI7411BWKR/@@download/IGVFFI7411BWKR.fastq.gz",
"md5sum": "e72f09a5bf166b85b4e643c0264374e3",
"s3_uri": "s3://igvf-files/2025/01/14/cf0ac7d8-fe6d-4977-87f2-a7b8bcf7c078/IGVFFI7411BWKR.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///LW429_S5_L004_R1_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/IGVFSM7766HOYF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7766HOYF",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW429"
],
"cellular_sub_pool": "subpool_LW429",
"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_LW429) 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": "2025-01-14T21:29:41.252065+00:00",
"submitter_comment": "Transcriptiome for LW429",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "d7d4bc20-2f4b-43dd-b04e-48463ada6bda"
}