{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7818HFMO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7818HFMO",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_LW435"
],
"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 [IGVFDS9289FWZN](/auxiliary-sets/IGVFDS9289FWZN/) has sequence file(s): [IGVFFI8547HGDV](/sequence-files/IGVFFI8547HGDV/), [IGVFFI0312LDQL](/sequence-files/IGVFFI0312LDQL/), [IGVFFI9725RURB](/sequence-files/IGVFFI9725RURB/), [IGVFFI9965CSOU](/sequence-files/IGVFFI9965CSOU/) 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/IGVFDS9289FWZN/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7818HFMO](/measurement-sets/IGVFDS7818HFMO/) has sequence file(s): [IGVFFI1994YPNP](/sequence-files/IGVFFI1994YPNP/), [IGVFFI0266LNZW](/sequence-files/IGVFFI0266LNZW/), [IGVFFI9977BZMF](/sequence-files/IGVFFI9977BZMF/), [IGVFFI7972XHRF](/sequence-files/IGVFFI7972XHRF/) 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/IGVFDS7818HFMO/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7818HFMO](/measurement-sets/IGVFDS7818HFMO/) has a sequence file [IGVFFI0266LNZW](/sequence-files/IGVFFI0266LNZW/) 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/IGVFDS7818HFMO/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS7818HFMO](/measurement-sets/IGVFDS7818HFMO/) has a sequence file [IGVFFI7972XHRF](/sequence-files/IGVFFI7972XHRF/) 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/IGVFDS7818HFMO/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS7818HFMO](/measurement-sets/IGVFDS7818HFMO/) 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/IGVFDS7818HFMO/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3881UZJT](/auxiliary-sets/IGVFDS3881UZJT/) has sequence file(s): [IGVFFI8257WJQZ](/sequence-files/IGVFFI8257WJQZ/), [IGVFFI7650HNVF](/sequence-files/IGVFFI7650HNVF/), [IGVFFI5492QZLT](/sequence-files/IGVFFI5492QZLT/), [IGVFFI5457CMID](/sequence-files/IGVFFI5457CMID/) 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/IGVFDS3881UZJT/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3881UZJT/",
"accession": "IGVFDS3881UZJT",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_sgRNA_LW435"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS9289FWZN/",
"accession": "IGVFDS9289FWZN",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_HTO_LW435"
],
"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": "2024-08-16T20:32:10.437281+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/IGVFFI1994YPNP/",
"accession": "IGVFFI1994YPNP",
"aliases": [
"gary-hon:LW435_5_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T20:59:59.849695+00:00",
"file_format": "fastq",
"file_size": 3540357966,
"href": "/sequence-files/IGVFFI1994YPNP/@@download/IGVFFI1994YPNP.fastq.gz",
"md5sum": "8c3a5992593efd95432a7113ee90cc3c",
"s3_uri": "s3://igvf-files/2024/11/13/a46e0c0b-57e9-4859-babc-f6f4bb29c1d1/IGVFFI1994YPNP.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//LW435_S4_L005_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0266LNZW/",
"accession": "IGVFFI0266LNZW",
"aliases": [
"gary-hon:LW435_5_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:00:44.680390+00:00",
"file_format": "fastq",
"file_size": 45491387629,
"href": "/sequence-files/IGVFFI0266LNZW/@@download/IGVFFI0266LNZW.fastq.gz",
"md5sum": "979c89c2d657db50b06cc3291c068c2e",
"s3_uri": "s3://igvf-files/2024/11/13/8b70848b-ed13-4528-83cb-da589af827d6/IGVFFI0266LNZW.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//LW435_S4_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9977BZMF/",
"accession": "IGVFFI9977BZMF",
"aliases": [
"gary-hon:LW435_5_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T20:59:18.499643+00:00",
"file_format": "fastq",
"file_size": 3508627029,
"href": "/sequence-files/IGVFFI9977BZMF/@@download/IGVFFI9977BZMF.fastq.gz",
"md5sum": "ff15f6f7b45363c55696a89110c730fc",
"s3_uri": "s3://igvf-files/2024/11/13/1ef6fce1-d7f9-451a-9953-8736518e8151/IGVFFI9977BZMF.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//LW435_S4_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7972XHRF/",
"accession": "IGVFFI7972XHRF",
"aliases": [
"gary-hon:LW435_5_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:07:32.408312+00:00",
"file_format": "fastq",
"file_size": 45879481490,
"href": "/sequence-files/IGVFFI7972XHRF/@@download/IGVFFI7972XHRF.fastq.gz",
"md5sum": "2c5e178a38838577c477a89d6fb73e4c",
"s3_uri": "s3://igvf-files/2024/11/13/78c56e54-63ed-437b-95e3-acf43194c16c/IGVFFI7972XHRF.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//LW435_S4_L005_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4252LFRU/"
],
"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/IGVFSM4418NJET/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4418NJET",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_PB9_LW435"
],
"cellular_sub_pool": "subpool_LW435",
"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_LW435) modified with CRISPRi Sp-dCas9, 3 week(s) after transfection 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": "2024-11-13T19:54:25.586415+00:00",
"submitter_comment": "Transcriptiome for LW435",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "b68f52a3-f3cc-40bf-87a5-df91bf3d97a7"
}