{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9005AVSB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9005AVSB",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW232"
],
"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 sequencing kit",
"detail": "Measurement set [IGVFDS9005AVSB](/measurement-sets/IGVFDS9005AVSB/) has sequence file(s) [IGVFFI8186QNKB](/sequence-files/IGVFFI8186QNKB/), [IGVFFI5849QWYL](/sequence-files/IGVFFI5849QWYL/), [IGVFFI7835UHSD](/sequence-files/IGVFFI7835UHSD/), [IGVFFI2485HZST](/sequence-files/IGVFFI2485HZST/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih single cell data should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS9005AVSB/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9005AVSB](/measurement-sets/IGVFDS9005AVSB/) has sequence file(s): [IGVFFI8186QNKB](/sequence-files/IGVFFI8186QNKB/), [IGVFFI5849QWYL](/sequence-files/IGVFFI5849QWYL/), [IGVFFI7835UHSD](/sequence-files/IGVFFI7835UHSD/), [IGVFFI2485HZST](/sequence-files/IGVFFI2485HZST/) 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/IGVFDS9005AVSB/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9005AVSB](/measurement-sets/IGVFDS9005AVSB/) has a sequence file [IGVFFI8186QNKB](/sequence-files/IGVFFI8186QNKB/) 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/IGVFDS9005AVSB/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9005AVSB](/measurement-sets/IGVFDS9005AVSB/) has a sequence file [IGVFFI2485HZST](/sequence-files/IGVFFI2485HZST/) 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/IGVFDS9005AVSB/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS9005AVSB](/measurement-sets/IGVFDS9005AVSB/) 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/IGVFDS9005AVSB/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS9005AVSB](/measurement-sets/IGVFDS9005AVSB/) 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/IGVFDS9005AVSB/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8202GWXE](/auxiliary-sets/IGVFDS8202GWXE/) has sequence file(s) [IGVFFI3533OPFH](/sequence-files/IGVFFI3533OPFH/), [IGVFFI4177QZAY](/sequence-files/IGVFFI4177QZAY/), [IGVFFI5494QEZY](/sequence-files/IGVFFI5494QEZY/), [IGVFFI0174OYDP](/sequence-files/IGVFFI0174OYDP/), [IGVFFI2826DJRC](/sequence-files/IGVFFI2826DJRC/), [IGVFFI8476XMZO](/sequence-files/IGVFFI8476XMZO/), [IGVFFI3449QVQP](/sequence-files/IGVFFI3449QVQP/), [IGVFFI5474JBFR](/sequence-files/IGVFFI5474JBFR/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih single cell data should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS8202GWXE/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8202GWXE](/auxiliary-sets/IGVFDS8202GWXE/) has sequence file(s): [IGVFFI3533OPFH](/sequence-files/IGVFFI3533OPFH/), [IGVFFI4177QZAY](/sequence-files/IGVFFI4177QZAY/), [IGVFFI5494QEZY](/sequence-files/IGVFFI5494QEZY/), [IGVFFI0174OYDP](/sequence-files/IGVFFI0174OYDP/), [IGVFFI2826DJRC](/sequence-files/IGVFFI2826DJRC/), [IGVFFI8476XMZO](/sequence-files/IGVFFI8476XMZO/), [IGVFFI3449QVQP](/sequence-files/IGVFFI3449QVQP/), [IGVFFI5474JBFR](/sequence-files/IGVFFI5474JBFR/) 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/IGVFDS8202GWXE/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0019ZVVN](/auxiliary-sets/IGVFDS0019ZVVN/) has sequence file(s) [IGVFFI6307ZDPG](/sequence-files/IGVFFI6307ZDPG/), [IGVFFI2739CHPC](/sequence-files/IGVFFI2739CHPC/), [IGVFFI5906NTWL](/sequence-files/IGVFFI5906NTWL/), [IGVFFI9506XCZX](/sequence-files/IGVFFI9506XCZX/), [IGVFFI7493FEQQ](/sequence-files/IGVFFI7493FEQQ/), [IGVFFI7011YGKB](/sequence-files/IGVFFI7011YGKB/), [IGVFFI9497SCBF](/sequence-files/IGVFFI9497SCBF/), [IGVFFI7480GPXJ](/sequence-files/IGVFFI7480GPXJ/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih single cell data should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS0019ZVVN/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0019ZVVN](/auxiliary-sets/IGVFDS0019ZVVN/) has sequence file(s): [IGVFFI6307ZDPG](/sequence-files/IGVFFI6307ZDPG/), [IGVFFI2739CHPC](/sequence-files/IGVFFI2739CHPC/), [IGVFFI5906NTWL](/sequence-files/IGVFFI5906NTWL/), [IGVFFI9506XCZX](/sequence-files/IGVFFI9506XCZX/), [IGVFFI7493FEQQ](/sequence-files/IGVFFI7493FEQQ/), [IGVFFI7011YGKB](/sequence-files/IGVFFI7011YGKB/), [IGVFFI9497SCBF](/sequence-files/IGVFFI9497SCBF/), [IGVFFI7480GPXJ](/sequence-files/IGVFFI7480GPXJ/) 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/IGVFDS0019ZVVN/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0019ZVVN/",
"accession": "IGVFDS0019ZVVN",
"aliases": [
"gary-hon:CM_Pilot_2_PB_HTO_LW232"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS8202GWXE/",
"accession": "IGVFDS8202GWXE",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW232"
],
"file_set_type": "gRNA 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/IGVFDS9629YZLO/",
"accession": "IGVFDS9629YZLO",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI4543YHDW/",
"accession": "IGVFFI4543YHDW",
"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": "2024-02-15T23:43:12.390554+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/IGVFFI8186QNKB/",
"accession": "IGVFFI8186QNKB",
"aliases": [
"gary-hon:LW232_4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:05:11.004643+00:00",
"file_format": "fastq",
"file_size": 19906842750,
"href": "/sequence-files/IGVFFI8186QNKB/@@download/IGVFFI8186QNKB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/a5e0e46c-4678-458b-8d91-9fd34ef499c7/IGVFFI8186QNKB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-22-McDermott-NovaSeq.10X/10X/LW232_S4_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5849QWYL/",
"accession": "IGVFFI5849QWYL",
"aliases": [
"gary-hon:LW232_4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:01:54.620331+00:00",
"file_format": "fastq",
"file_size": 1586306971,
"href": "/sequence-files/IGVFFI5849QWYL/@@download/IGVFFI5849QWYL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/a642caed-e1cb-42b5-a22e-2164eef32085/IGVFFI5849QWYL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-22-McDermott-NovaSeq.10X/10X/LW232_S4_L004_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7835UHSD/",
"accession": "IGVFFI7835UHSD",
"aliases": [
"gary-hon:LW232_4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:01:35.599659+00:00",
"file_format": "fastq",
"file_size": 1555880579,
"href": "/sequence-files/IGVFFI7835UHSD/@@download/IGVFFI7835UHSD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/a875ab35-7ea2-40e8-b98a-86bcf07ac5b5/IGVFFI7835UHSD.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-22-McDermott-NovaSeq.10X/10X/LW232_S4_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2485HZST/",
"accession": "IGVFFI2485HZST",
"aliases": [
"gary-hon:LW232_4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T20:02:13.417239+00:00",
"file_format": "fastq",
"file_size": 20006501072,
"href": "/sequence-files/IGVFFI2485HZST/@@download/IGVFFI2485HZST.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/7ed4e72b-9bb6-48f4-9f6c-19adbe0dbfc8/IGVFFI2485HZST.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-22-McDermott-NovaSeq.10X/10X/LW232_S4_L004_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9192YMGI/"
],
"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/IGVFSM4953FLXN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4953FLXN",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW232"
],
"cellular_sub_pool": "subpool_LW262",
"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_LW262) 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": "2024-02-21T18:19:38.935555+00:00",
"submitter_comment": "Transcriptiome for LW232'",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "c06a9035-41a3-4278-9921-4a68ed4ad402"
}