{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2827ZGPM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2827ZGPM",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW430"
],
"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 [IGVFDS3215JVHK](/auxiliary-sets/IGVFDS3215JVHK/) has sequence file(s): [IGVFFI1560JLBB](/sequence-files/IGVFFI1560JLBB/), [IGVFFI4286UWSC](/sequence-files/IGVFFI4286UWSC/), [IGVFFI1103OELL](/sequence-files/IGVFFI1103OELL/), [IGVFFI1203FMSV](/sequence-files/IGVFFI1203FMSV/) 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/IGVFDS3215JVHK/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2827ZGPM](/measurement-sets/IGVFDS2827ZGPM/) has sequence file(s): [IGVFFI5203QBQH](/sequence-files/IGVFFI5203QBQH/), [IGVFFI6198SDVJ](/sequence-files/IGVFFI6198SDVJ/), [IGVFFI9982SPGL](/sequence-files/IGVFFI9982SPGL/), [IGVFFI7547SCMX](/sequence-files/IGVFFI7547SCMX/) 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/IGVFDS2827ZGPM/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2827ZGPM](/measurement-sets/IGVFDS2827ZGPM/) has a sequence file [IGVFFI5203QBQH](/sequence-files/IGVFFI5203QBQH/) 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/IGVFDS2827ZGPM/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2827ZGPM](/measurement-sets/IGVFDS2827ZGPM/) has a sequence file [IGVFFI6198SDVJ](/sequence-files/IGVFFI6198SDVJ/) 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/IGVFDS2827ZGPM/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS2827ZGPM](/measurement-sets/IGVFDS2827ZGPM/) 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/IGVFDS2827ZGPM/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS2827ZGPM](/measurement-sets/IGVFDS2827ZGPM/) has an `assay_term` of in vitro CRISPR screen using single-cell RNA-seq but no `onlist_files` nor `onlist_methods`. Measurement sets to be processed via the single cell uniform pipeline are expected to have onlist files and onlist methods indicated.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_onlist",
"path": "/measurement-sets/IGVFDS2827ZGPM/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1672IHVM](/auxiliary-sets/IGVFDS1672IHVM/) has sequence file(s): [IGVFFI5354EYBB](/sequence-files/IGVFFI5354EYBB/), [IGVFFI5190ALBH](/sequence-files/IGVFFI5190ALBH/), [IGVFFI3295XOIB](/sequence-files/IGVFFI3295XOIB/), [IGVFFI7350HFKN](/sequence-files/IGVFFI7350HFKN/) 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/IGVFDS1672IHVM/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1672IHVM/",
"accession": "IGVFDS1672IHVM",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_sgRNA_LW430"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3215JVHK/",
"accession": "IGVFDS3215JVHK",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_HTO_LW430"
],
"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": "2024-08-16T20:32:01.810208+00:00",
"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/IGVFFI5203QBQH/",
"accession": "IGVFFI5203QBQH",
"aliases": [
"gary-hon:LW430_4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T22:08:09.137092+00:00",
"file_format": "fastq",
"file_size": 34862740279,
"href": "/sequence-files/IGVFFI5203QBQH/@@download/IGVFFI5203QBQH.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/14/2ef88311-71d5-41e5-8285-dceb0ba65e11/IGVFFI5203QBQH.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///LW430_S6_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6198SDVJ/",
"accession": "IGVFFI6198SDVJ",
"aliases": [
"gary-hon:LW430_4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T22:13:20.538642+00:00",
"file_format": "fastq",
"file_size": 35324648901,
"href": "/sequence-files/IGVFFI6198SDVJ/@@download/IGVFFI6198SDVJ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/14/8e8c2480-fe0b-481a-97c2-351b2a4d5f76/IGVFFI6198SDVJ.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///LW430_S6_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9982SPGL/",
"accession": "IGVFFI9982SPGL",
"aliases": [
"gary-hon:LW430_4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T22:07:03.268815+00:00",
"file_format": "fastq",
"file_size": 2770480128,
"href": "/sequence-files/IGVFFI9982SPGL/@@download/IGVFFI9982SPGL.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/14/463a4ef2-11c0-4682-8e5e-50cdc5aae90a/IGVFFI9982SPGL.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///LW430_S6_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7547SCMX/",
"accession": "IGVFFI7547SCMX",
"aliases": [
"gary-hon:LW430_4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-01-14T22:07:35.898722+00:00",
"file_format": "fastq",
"file_size": 2639002007,
"href": "/sequence-files/IGVFFI7547SCMX/@@download/IGVFFI7547SCMX.fastq.gz",
"s3_uri": "s3://igvf-files/2025/01/14/f01660b6-b953-4759-8356-45b5da46693f/IGVFFI7547SCMX.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///LW430_S6_L004_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5498SDRJ/"
],
"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/IGVFSM2127MVQH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2127MVQH",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW430"
],
"cellular_sub_pool": "subpool_LW430",
"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_LW430) 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": "2025-01-14T21:31:32.570608+00:00",
"submitter_comment": "Transcriptiome for LW430",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "3d7a9d28-9aaf-4974-afa7-02cd5d1c8b3f"
}