{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9614JGLX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9614JGLX",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_LW437"
],
"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 [IGVFDS8878JVPZ](/auxiliary-sets/IGVFDS8878JVPZ/) has sequence file(s): [IGVFFI1394EWKL](/sequence-files/IGVFFI1394EWKL/), [IGVFFI7023BMQV](/sequence-files/IGVFFI7023BMQV/), [IGVFFI8600ACAI](/sequence-files/IGVFFI8600ACAI/), [IGVFFI1686TDZN](/sequence-files/IGVFFI1686TDZN/) 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/IGVFDS8878JVPZ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1417TPKZ](/auxiliary-sets/IGVFDS1417TPKZ/) has sequence file(s): [IGVFFI9007JSBK](/sequence-files/IGVFFI9007JSBK/), [IGVFFI6210OCQP](/sequence-files/IGVFFI6210OCQP/), [IGVFFI9606HEAN](/sequence-files/IGVFFI9606HEAN/), [IGVFFI9049KFCN](/sequence-files/IGVFFI9049KFCN/) 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/IGVFDS1417TPKZ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9614JGLX](/measurement-sets/IGVFDS9614JGLX/) has sequence file(s): [IGVFFI6775MOMC](/sequence-files/IGVFFI6775MOMC/), [IGVFFI5747FEKP](/sequence-files/IGVFFI5747FEKP/), [IGVFFI7723HURE](/sequence-files/IGVFFI7723HURE/), [IGVFFI2630YDCC](/sequence-files/IGVFFI2630YDCC/) 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/IGVFDS9614JGLX/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9614JGLX](/measurement-sets/IGVFDS9614JGLX/) has a sequence file [IGVFFI5747FEKP](/sequence-files/IGVFFI5747FEKP/) 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/IGVFDS9614JGLX/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9614JGLX](/measurement-sets/IGVFDS9614JGLX/) has a sequence file [IGVFFI7723HURE](/sequence-files/IGVFFI7723HURE/) 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/IGVFDS9614JGLX/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS9614JGLX](/measurement-sets/IGVFDS9614JGLX/) 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/IGVFDS9614JGLX/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1417TPKZ/",
"accession": "IGVFDS1417TPKZ",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_sgRNA_LW437"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS8878JVPZ/",
"accession": "IGVFDS8878JVPZ",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_HTO_LW437"
],
"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": "2024-08-16T20:32:13.618519+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/IGVFFI6775MOMC/",
"accession": "IGVFFI6775MOMC",
"aliases": [
"gary-hon:LW437_5_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:27:05.888041+00:00",
"file_format": "fastq",
"file_size": 3513748477,
"href": "/sequence-files/IGVFFI6775MOMC/@@download/IGVFFI6775MOMC.fastq.gz",
"md5sum": "9059d53b249e2c2e0a77a2a19a328871",
"s3_uri": "s3://igvf-files/2024/11/13/6fa79eaf-eb28-46ed-a520-8870d546bba0/IGVFFI6775MOMC.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//LW437_S6_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5747FEKP/",
"accession": "IGVFFI5747FEKP",
"aliases": [
"gary-hon:LW437_5_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:28:27.463123+00:00",
"file_format": "fastq",
"file_size": 39894748258,
"href": "/sequence-files/IGVFFI5747FEKP/@@download/IGVFFI5747FEKP.fastq.gz",
"md5sum": "2bfbff238ff0d162f0827bd2ab91488f",
"s3_uri": "s3://igvf-files/2024/11/13/032dd973-164e-4205-9e46-dfca8e534657/IGVFFI5747FEKP.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//LW437_S6_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7723HURE/",
"accession": "IGVFFI7723HURE",
"aliases": [
"gary-hon:LW437_5_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:34:25.846553+00:00",
"file_format": "fastq",
"file_size": 39895220071,
"href": "/sequence-files/IGVFFI7723HURE/@@download/IGVFFI7723HURE.fastq.gz",
"md5sum": "09f2d0ace364bff2d41ecbb91d4d0a32",
"s3_uri": "s3://igvf-files/2024/11/13/68b29624-965f-4562-8a48-881627eb823a/IGVFFI7723HURE.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//LW437_S6_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2630YDCC/",
"accession": "IGVFFI2630YDCC",
"aliases": [
"gary-hon:LW437_5_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:27:50.654470+00:00",
"file_format": "fastq",
"file_size": 2961081081,
"href": "/sequence-files/IGVFFI2630YDCC/@@download/IGVFFI2630YDCC.fastq.gz",
"md5sum": "41dca0a872c033e28b94dd2a39568639",
"s3_uri": "s3://igvf-files/2024/11/13/aae12dc4-11c4-4398-be2b-8512708163d1/IGVFFI2630YDCC.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//LW437_S6_L005_I2_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/IGVFSM8072YOLO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8072YOLO",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_PB9_LW437"
],
"cellular_sub_pool": "subpool_LW437",
"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_LW437) 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": "2024-11-13T19:58:30.099122+00:00",
"submitter_comment": "Transcriptiome for LW437",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "a9f3aefe-2b4e-44a3-adee-bec39811c512"
}