{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4615AXMO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4615AXMO",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_LW436"
],
"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 [IGVFDS9781HZZV](/auxiliary-sets/IGVFDS9781HZZV/) has a sequence file [IGVFFI1163JWIL](/sequence-files/IGVFFI1163JWIL/) 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/IGVFDS9781HZZV/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS9781HZZV](/auxiliary-sets/IGVFDS9781HZZV/) has a sequence file [IGVFFI5776RSQZ](/sequence-files/IGVFFI5776RSQZ/) 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/IGVFDS9781HZZV/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS9781HZZV](/auxiliary-sets/IGVFDS9781HZZV/) has a sequence file [IGVFFI2584JXRS](/sequence-files/IGVFFI2584JXRS/) 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/IGVFDS9781HZZV/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS9781HZZV](/auxiliary-sets/IGVFDS9781HZZV/) has a sequence file [IGVFFI0178AEKX](/sequence-files/IGVFFI0178AEKX/) 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/IGVFDS9781HZZV/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS5210TKRS](/auxiliary-sets/IGVFDS5210TKRS/) has a sequence file [IGVFFI1889WATW](/sequence-files/IGVFFI1889WATW/) 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/IGVFDS5210TKRS/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS5210TKRS](/auxiliary-sets/IGVFDS5210TKRS/) has a sequence file [IGVFFI0936YGAN](/sequence-files/IGVFFI0936YGAN/) 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/IGVFDS5210TKRS/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS5210TKRS](/auxiliary-sets/IGVFDS5210TKRS/) has a sequence file [IGVFFI9720JHJW](/sequence-files/IGVFFI9720JHJW/) 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/IGVFDS5210TKRS/"
},
{
"category": "inconsistent sequencing kit",
"detail": "Auxiliary set [IGVFDS5210TKRS](/auxiliary-sets/IGVFDS5210TKRS/) has a sequence file [IGVFFI3170CQKI](/sequence-files/IGVFFI3170CQKI/) 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/IGVFDS5210TKRS/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9781HZZV](/auxiliary-sets/IGVFDS9781HZZV/) has sequence file(s): [IGVFFI1163JWIL](/sequence-files/IGVFFI1163JWIL/), [IGVFFI5776RSQZ](/sequence-files/IGVFFI5776RSQZ/), [IGVFFI2584JXRS](/sequence-files/IGVFFI2584JXRS/), [IGVFFI0178AEKX](/sequence-files/IGVFFI0178AEKX/) 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/IGVFDS9781HZZV/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4615AXMO](/measurement-sets/IGVFDS4615AXMO/) has sequence file(s): [IGVFFI7391DKIW](/sequence-files/IGVFFI7391DKIW/), [IGVFFI0616HDUP](/sequence-files/IGVFFI0616HDUP/), [IGVFFI8911SHCH](/sequence-files/IGVFFI8911SHCH/), [IGVFFI5764VRNL](/sequence-files/IGVFFI5764VRNL/) 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/IGVFDS4615AXMO/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5210TKRS](/auxiliary-sets/IGVFDS5210TKRS/) has sequence file(s): [IGVFFI1889WATW](/sequence-files/IGVFFI1889WATW/), [IGVFFI0936YGAN](/sequence-files/IGVFFI0936YGAN/), [IGVFFI9720JHJW](/sequence-files/IGVFFI9720JHJW/), [IGVFFI3170CQKI](/sequence-files/IGVFFI3170CQKI/) 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/IGVFDS5210TKRS/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9781HZZV/",
"accession": "IGVFDS9781HZZV",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_sgRNA_LW436"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS5210TKRS/",
"accession": "IGVFDS5210TKRS",
"aliases": [
"gary-hon:differentited_WTC11_CM_Pilot2_Mini_PB9_HTO_LW436"
],
"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": "2024-08-16T20:32:11.907519+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/IGVFFI7391DKIW/",
"accession": "IGVFFI7391DKIW",
"aliases": [
"gary-hon:LW436_5_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:21:19.552888+00:00",
"file_format": "fastq",
"file_size": 38393200595,
"href": "/sequence-files/IGVFFI7391DKIW/@@download/IGVFFI7391DKIW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/a0566df8-30af-4456-80f0-d739889c58a1/IGVFFI7391DKIW.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//LW436_S5_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0616HDUP/",
"accession": "IGVFFI0616HDUP",
"aliases": [
"gary-hon:LW436_5_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:15:00.683965+00:00",
"file_format": "fastq",
"file_size": 2780741983,
"href": "/sequence-files/IGVFFI0616HDUP/@@download/IGVFFI0616HDUP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/0dae1842-e918-4ef8-8195-4df032ad237c/IGVFFI0616HDUP.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//LW436_S5_L005_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8911SHCH/",
"accession": "IGVFFI8911SHCH",
"aliases": [
"gary-hon:LW436_5_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:14:21.312531+00:00",
"file_format": "fastq",
"file_size": 3121749920,
"href": "/sequence-files/IGVFFI8911SHCH/@@download/IGVFFI8911SHCH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/31c3e8b9-033c-4249-b67b-d02f9bc6249a/IGVFFI8911SHCH.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//LW436_S5_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5764VRNL/",
"accession": "IGVFFI5764VRNL",
"aliases": [
"gary-hon:LW436_5_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T21:15:37.677403+00:00",
"file_format": "fastq",
"file_size": 38134802716,
"href": "/sequence-files/IGVFFI5764VRNL/@@download/IGVFFI5764VRNL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/13/8c930429-a7cb-4c3b-98c7-ded0fc5a224d/IGVFFI5764VRNL.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//LW436_S5_L005_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4252LFRU/"
],
"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/IGVFSM8889XSOR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8889XSOR",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot2_Mini_PB9_LW436"
],
"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_LW436), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected 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": "2024-11-13T19:56:25.010147+00:00",
"submitter_comment": "Transcriptiome for LW436",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "85e9940b-fa17-42df-aff4-593636a42360"
}