{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6863PGGX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6863PGGX",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW427"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003660/",
"status": "released",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"audit": {
"ERROR": [
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS5699EGGK](/auxiliary-sets/IGVFDS5699EGGK/) has a sequence file [IGVFFI1042XEFF](/sequence-files/IGVFFI1042XEFF/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
"level": 60,
"level_name": "ERROR",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS5699EGGK/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS5699EGGK](/auxiliary-sets/IGVFDS5699EGGK/) has a sequence file [IGVFFI7040RYGM](/sequence-files/IGVFFI7040RYGM/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
"level": 60,
"level_name": "ERROR",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS5699EGGK/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS5699EGGK](/auxiliary-sets/IGVFDS5699EGGK/) has a sequence file [IGVFFI2605PQQK](/sequence-files/IGVFFI2605PQQK/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
"level": 60,
"level_name": "ERROR",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS5699EGGK/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS5699EGGK](/auxiliary-sets/IGVFDS5699EGGK/) has a sequence file [IGVFFI0411GLKE](/sequence-files/IGVFFI0411GLKE/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
"level": 60,
"level_name": "ERROR",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS5699EGGK/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS0465GFSG](/auxiliary-sets/IGVFDS0465GFSG/) has a sequence file [IGVFFI5575KDRV](/sequence-files/IGVFFI5575KDRV/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
"level": 60,
"level_name": "ERROR",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS0465GFSG/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS0465GFSG](/auxiliary-sets/IGVFDS0465GFSG/) has a sequence file [IGVFFI4151SZSL](/sequence-files/IGVFFI4151SZSL/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
"level": 60,
"level_name": "ERROR",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS0465GFSG/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS0465GFSG](/auxiliary-sets/IGVFDS0465GFSG/) has a sequence file [IGVFFI5902FATE](/sequence-files/IGVFFI5902FATE/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
"level": 60,
"level_name": "ERROR",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS0465GFSG/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS0465GFSG](/auxiliary-sets/IGVFDS0465GFSG/) has a sequence file [IGVFFI2355JSHD](/sequence-files/IGVFFI2355JSHD/) sequenced on a `sequencing_platform` [EFO_0008637](/platform-terms/EFO_0008637/) that is inconsistent with its `sequencing_kit` NovaSeq X Series 25B Reagent Kit. Sequence files should specify a sequencing kit which is consistent with their sequencing platform. Sequence files in the same sequencing run should also specify the same sequencing kit.",
"level": 60,
"level_name": "ERROR",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS0465GFSG/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5699EGGK](/auxiliary-sets/IGVFDS5699EGGK/) has sequence file(s): [IGVFFI1042XEFF](/sequence-files/IGVFFI1042XEFF/), [IGVFFI7040RYGM](/sequence-files/IGVFFI7040RYGM/), [IGVFFI2605PQQK](/sequence-files/IGVFFI2605PQQK/), [IGVFFI0411GLKE](/sequence-files/IGVFFI0411GLKE/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS5699EGGK/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6863PGGX](/measurement-sets/IGVFDS6863PGGX/) has sequence file(s): [IGVFFI6800PCCO](/sequence-files/IGVFFI6800PCCO/), [IGVFFI3407PSDS](/sequence-files/IGVFFI3407PSDS/), [IGVFFI5941BIXV](/sequence-files/IGVFFI5941BIXV/), [IGVFFI4912HSIZ](/sequence-files/IGVFFI4912HSIZ/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS6863PGGX/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0465GFSG](/auxiliary-sets/IGVFDS0465GFSG/) has sequence file(s): [IGVFFI5575KDRV](/sequence-files/IGVFFI5575KDRV/), [IGVFFI4151SZSL](/sequence-files/IGVFFI4151SZSL/), [IGVFFI5902FATE](/sequence-files/IGVFFI5902FATE/), [IGVFFI2355JSHD](/sequence-files/IGVFFI2355JSHD/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS0465GFSG/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0465GFSG/",
"accession": "IGVFDS0465GFSG",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_sgRNA_LW427"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS5699EGGK/",
"accession": "IGVFDS5699EGGK",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_LPv4_HTO_LW427"
],
"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"
},
"control_for": [],
"creation_timestamp": "2024-08-16T20:31:52.045976+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/IGVFFI6800PCCO/",
"accession": "IGVFFI6800PCCO",
"aliases": [
"gary-hon:LW427_4_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-20T21:06:01.883872+00:00",
"file_format": "fastq",
"file_size": 3101307243,
"href": "/sequence-files/IGVFFI6800PCCO/@@download/IGVFFI6800PCCO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/20/9fda2044-c2cf-4256-a362-07a179661360/IGVFFI6800PCCO.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///LW427_S3_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3407PSDS/",
"accession": "IGVFFI3407PSDS",
"aliases": [
"gary-hon:LW427_4_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-20T21:06:37.362586+00:00",
"file_format": "fastq",
"file_size": 3323150667,
"href": "/sequence-files/IGVFFI3407PSDS/@@download/IGVFFI3407PSDS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/20/951aa01a-2ecf-4729-9174-58c05b0fab26/IGVFFI3407PSDS.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///LW427_S3_L004_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5941BIXV/",
"accession": "IGVFFI5941BIXV",
"aliases": [
"gary-hon:LW427_4_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-20T21:07:13.658030+00:00",
"file_format": "fastq",
"file_size": 43228498843,
"href": "/sequence-files/IGVFFI5941BIXV/@@download/IGVFFI5941BIXV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/20/d389bfc3-4b38-45a4-99c9-56db5358cd7a/IGVFFI5941BIXV.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///LW427_S3_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4912HSIZ/",
"accession": "IGVFFI4912HSIZ",
"aliases": [
"gary-hon:LW427_4_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-20T21:13:32.417520+00:00",
"file_format": "fastq",
"file_size": 43676184633,
"href": "/sequence-files/IGVFFI4912HSIZ/@@download/IGVFFI4912HSIZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/20/2845c96d-ad56-4549-915a-dc2c7b1094dc/IGVFFI4912HSIZ.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///LW427_S3_L004_R2_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/IGVFSM0565MLZG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0565MLZG",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_LPv4_LW427"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS0346MQBH/",
"accession": "IGVFDS0346MQBH",
"file_set_type": "guide library",
"status": "preview",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"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": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW427), male, Homo sapiens 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": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-12-20T21:00:07.712594+00:00",
"submitter_comment": "Transcriptiome for LW427",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "4dccbacb-fd28-4d3b-861e-913892cbd6d6"
}