{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0262BREE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0262BREE",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW261"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003660/",
"status": "released",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7783CMAZ](/auxiliary-sets/IGVFDS7783CMAZ/) has sequence file(s) [IGVFFI4960KIPY](/sequence-files/IGVFFI4960KIPY/), [IGVFFI0465HHKI](/sequence-files/IGVFFI0465HHKI/), [IGVFFI2358HDWU](/sequence-files/IGVFFI2358HDWU/), [IGVFFI0811GSLQ](/sequence-files/IGVFFI0811GSLQ/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS7783CMAZ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7783CMAZ](/auxiliary-sets/IGVFDS7783CMAZ/) has sequence file(s): [IGVFFI4960KIPY](/sequence-files/IGVFFI4960KIPY/), [IGVFFI0465HHKI](/sequence-files/IGVFFI0465HHKI/), [IGVFFI2358HDWU](/sequence-files/IGVFFI2358HDWU/), [IGVFFI0811GSLQ](/sequence-files/IGVFFI0811GSLQ/) 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/IGVFDS7783CMAZ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0262BREE](/measurement-sets/IGVFDS0262BREE/) has sequence file(s) [IGVFFI6482UUDY](/sequence-files/IGVFFI6482UUDY/), [IGVFFI5673JAWE](/sequence-files/IGVFFI5673JAWE/), [IGVFFI5023CDRX](/sequence-files/IGVFFI5023CDRX/), [IGVFFI0458UOKL](/sequence-files/IGVFFI0458UOKL/), [IGVFFI3649RJAY](/sequence-files/IGVFFI3649RJAY/), [IGVFFI4342WYGO](/sequence-files/IGVFFI4342WYGO/), [IGVFFI0141AYNM](/sequence-files/IGVFFI0141AYNM/), [IGVFFI8875BMHJ](/sequence-files/IGVFFI8875BMHJ/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS0262BREE/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0262BREE](/measurement-sets/IGVFDS0262BREE/) has sequence file(s): [IGVFFI6482UUDY](/sequence-files/IGVFFI6482UUDY/), [IGVFFI5673JAWE](/sequence-files/IGVFFI5673JAWE/), [IGVFFI5023CDRX](/sequence-files/IGVFFI5023CDRX/), [IGVFFI0458UOKL](/sequence-files/IGVFFI0458UOKL/), [IGVFFI3649RJAY](/sequence-files/IGVFFI3649RJAY/), [IGVFFI4342WYGO](/sequence-files/IGVFFI4342WYGO/), [IGVFFI0141AYNM](/sequence-files/IGVFFI0141AYNM/), [IGVFFI8875BMHJ](/sequence-files/IGVFFI8875BMHJ/) 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/IGVFDS0262BREE/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1373ALPP](/auxiliary-sets/IGVFDS1373ALPP/) has sequence file(s) [IGVFFI8947XMLR](/sequence-files/IGVFFI8947XMLR/), [IGVFFI4740QPJS](/sequence-files/IGVFFI4740QPJS/), [IGVFFI4786EANZ](/sequence-files/IGVFFI4786EANZ/), [IGVFFI7495WDFC](/sequence-files/IGVFFI7495WDFC/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS1373ALPP/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1373ALPP](/auxiliary-sets/IGVFDS1373ALPP/) has sequence file(s): [IGVFFI8947XMLR](/sequence-files/IGVFFI8947XMLR/), [IGVFFI4740QPJS](/sequence-files/IGVFFI4740QPJS/), [IGVFFI4786EANZ](/sequence-files/IGVFFI4786EANZ/), [IGVFFI7495WDFC](/sequence-files/IGVFFI7495WDFC/) 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/IGVFDS1373ALPP/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7783CMAZ/",
"accession": "IGVFDS7783CMAZ",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW261"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS1373ALPP/",
"accession": "IGVFDS1373ALPP",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW261"
],
"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"
},
"control_for": [],
"creation_timestamp": "2024-02-15T23:43:20.830909+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/IGVFFI6482UUDY/",
"accession": "IGVFFI6482UUDY",
"aliases": [
"gary-hon:LW261_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:47:55.945063+00:00",
"file_format": "fastq",
"file_size": 546643462,
"href": "/sequence-files/IGVFFI6482UUDY/@@download/IGVFFI6482UUDY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/44e45bd5-3405-4669-a335-62701f3755ec/IGVFFI6482UUDY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW261_S1_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5673JAWE/",
"accession": "IGVFFI5673JAWE",
"aliases": [
"gary-hon:LW261_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:48:05.447006+00:00",
"file_format": "fastq",
"file_size": 528039440,
"href": "/sequence-files/IGVFFI5673JAWE/@@download/IGVFFI5673JAWE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/4a209b19-e2c5-4d6d-9592-c49f59112621/IGVFFI5673JAWE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW261_S1_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5023CDRX/",
"accession": "IGVFFI5023CDRX",
"aliases": [
"gary-hon:LW261_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:48:14.047408+00:00",
"file_format": "fastq",
"file_size": 1828680501,
"href": "/sequence-files/IGVFFI5023CDRX/@@download/IGVFFI5023CDRX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/4d81362e-72bf-495e-aa4b-62c1474bc2cc/IGVFFI5023CDRX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW261_S1_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0458UOKL/",
"accession": "IGVFFI0458UOKL",
"aliases": [
"gary-hon:LW261_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:48:37.877899+00:00",
"file_format": "fastq",
"file_size": 4508972059,
"href": "/sequence-files/IGVFFI0458UOKL/@@download/IGVFFI0458UOKL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/318396e5-f381-40ab-b69b-035345021841/IGVFFI0458UOKL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW261_S1_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3649RJAY/",
"accession": "IGVFFI3649RJAY",
"aliases": [
"gary-hon:LW261_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:49:21.041177+00:00",
"file_format": "fastq",
"file_size": 569178908,
"href": "/sequence-files/IGVFFI3649RJAY/@@download/IGVFFI3649RJAY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/2d1cb902-0555-4bd1-a8a2-998c5bbd86ba/IGVFFI3649RJAY.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW261_S1_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4342WYGO/",
"accession": "IGVFFI4342WYGO",
"aliases": [
"gary-hon:LW261_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:49:30.280034+00:00",
"file_format": "fastq",
"file_size": 508572205,
"href": "/sequence-files/IGVFFI4342WYGO/@@download/IGVFFI4342WYGO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/e292c51d-db21-4c75-88ce-68f3fc48681c/IGVFFI4342WYGO.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW261_S1_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0141AYNM/",
"accession": "IGVFFI0141AYNM",
"aliases": [
"gary-hon:LW261_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:49:38.735519+00:00",
"file_format": "fastq",
"file_size": 1665556348,
"href": "/sequence-files/IGVFFI0141AYNM/@@download/IGVFFI0141AYNM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/9dee244b-1080-431e-bdc2-734fcddd4ff6/IGVFFI0141AYNM.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW261_S1_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8875BMHJ/",
"accession": "IGVFFI8875BMHJ",
"aliases": [
"gary-hon:LW261_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:49:57.218504+00:00",
"file_format": "fastq",
"file_size": 4166124945,
"href": "/sequence-files/IGVFFI8875BMHJ/@@download/IGVFFI8875BMHJ.fastq.gz",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-13-McDermott-NextSeq.10X.run3.transcriptome/2023-07-13/outs/fastq_path/AAC5GH5HV/LW261_S1_L002_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4003HZAB/"
],
"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/IGVFSM1972EKCJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1972EKCJ",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW261"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS9629YZLO/",
"accession": "IGVFDS9629YZLO",
"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_LW261), 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": "2024-02-20T17:47:55.945063+00:00",
"submitter_comment": "Transcriptiome for LW261'",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "05642a32-4377-4b02-9bc8-5ac17067a4bd"
}