{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4965SLDK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4965SLDK",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW263"
],
"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 [IGVFDS1349DIMY](/auxiliary-sets/IGVFDS1349DIMY/) has sequence file(s) [IGVFFI5886EXSK](/sequence-files/IGVFFI5886EXSK/), [IGVFFI5666YZNA](/sequence-files/IGVFFI5666YZNA/), [IGVFFI4467KSXD](/sequence-files/IGVFFI4467KSXD/), [IGVFFI0207DWDS](/sequence-files/IGVFFI0207DWDS/) 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/IGVFDS1349DIMY/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1349DIMY](/auxiliary-sets/IGVFDS1349DIMY/) has sequence file(s): [IGVFFI5886EXSK](/sequence-files/IGVFFI5886EXSK/), [IGVFFI5666YZNA](/sequence-files/IGVFFI5666YZNA/), [IGVFFI4467KSXD](/sequence-files/IGVFFI4467KSXD/), [IGVFFI0207DWDS](/sequence-files/IGVFFI0207DWDS/) 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/IGVFDS1349DIMY/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3499IMSW](/auxiliary-sets/IGVFDS3499IMSW/) has sequence file(s) [IGVFFI3413ZJXI](/sequence-files/IGVFFI3413ZJXI/), [IGVFFI7275XULX](/sequence-files/IGVFFI7275XULX/), [IGVFFI8393MYLT](/sequence-files/IGVFFI8393MYLT/), [IGVFFI7485JXZQ](/sequence-files/IGVFFI7485JXZQ/) 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/IGVFDS3499IMSW/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3499IMSW](/auxiliary-sets/IGVFDS3499IMSW/) has sequence file(s): [IGVFFI3413ZJXI](/sequence-files/IGVFFI3413ZJXI/), [IGVFFI7275XULX](/sequence-files/IGVFFI7275XULX/), [IGVFFI8393MYLT](/sequence-files/IGVFFI8393MYLT/), [IGVFFI7485JXZQ](/sequence-files/IGVFFI7485JXZQ/) 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/IGVFDS3499IMSW/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4965SLDK](/measurement-sets/IGVFDS4965SLDK/) has sequence file(s) [IGVFFI3835DQFV](/sequence-files/IGVFFI3835DQFV/), [IGVFFI2480DXKX](/sequence-files/IGVFFI2480DXKX/), [IGVFFI9227QJVY](/sequence-files/IGVFFI9227QJVY/), [IGVFFI8530NRGN](/sequence-files/IGVFFI8530NRGN/), [IGVFFI6673PFDE](/sequence-files/IGVFFI6673PFDE/), [IGVFFI3950HPMX](/sequence-files/IGVFFI3950HPMX/), [IGVFFI5242ONUU](/sequence-files/IGVFFI5242ONUU/), [IGVFFI9286IOQJ](/sequence-files/IGVFFI9286IOQJ/) 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/IGVFDS4965SLDK/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4965SLDK](/measurement-sets/IGVFDS4965SLDK/) has sequence file(s): [IGVFFI3835DQFV](/sequence-files/IGVFFI3835DQFV/), [IGVFFI2480DXKX](/sequence-files/IGVFFI2480DXKX/), [IGVFFI9227QJVY](/sequence-files/IGVFFI9227QJVY/), [IGVFFI8530NRGN](/sequence-files/IGVFFI8530NRGN/), [IGVFFI6673PFDE](/sequence-files/IGVFFI6673PFDE/), [IGVFFI3950HPMX](/sequence-files/IGVFFI3950HPMX/), [IGVFFI5242ONUU](/sequence-files/IGVFFI5242ONUU/), [IGVFFI9286IOQJ](/sequence-files/IGVFFI9286IOQJ/) 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/IGVFDS4965SLDK/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3499IMSW/",
"accession": "IGVFDS3499IMSW",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW263"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS1349DIMY/",
"accession": "IGVFDS1349DIMY",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW263"
],
"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": "2024-02-15T23:43:22.918980+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/IGVFFI3835DQFV/",
"accession": "IGVFFI3835DQFV",
"aliases": [
"gary-hon:LW263_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:52:59.793968+00:00",
"file_format": "fastq",
"file_size": 464312119,
"href": "/sequence-files/IGVFFI3835DQFV/@@download/IGVFFI3835DQFV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/9314f008-fce7-4250-bb08-30ae4d5159f7/IGVFFI3835DQFV.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/LW263_S3_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2480DXKX/",
"accession": "IGVFFI2480DXKX",
"aliases": [
"gary-hon:LW263_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:53:08.016870+00:00",
"file_format": "fastq",
"file_size": 458230732,
"href": "/sequence-files/IGVFFI2480DXKX/@@download/IGVFFI2480DXKX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/1dd382d7-e4ee-44cf-9ef9-9d0e4c23b69c/IGVFFI2480DXKX.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/LW263_S3_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9227QJVY/",
"accession": "IGVFFI9227QJVY",
"aliases": [
"gary-hon:LW263_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:53:19.368361+00:00",
"file_format": "fastq",
"file_size": 1440579873,
"href": "/sequence-files/IGVFFI9227QJVY/@@download/IGVFFI9227QJVY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/205d739c-f7a4-42be-bbfe-a5ec5e39ea00/IGVFFI9227QJVY.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/LW263_S3_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8530NRGN/",
"accession": "IGVFFI8530NRGN",
"aliases": [
"gary-hon:LW263_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:53:35.981641+00:00",
"file_format": "fastq",
"file_size": 3539853202,
"href": "/sequence-files/IGVFFI8530NRGN/@@download/IGVFFI8530NRGN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/3a108809-966d-486c-8a5c-567441c74d4c/IGVFFI8530NRGN.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/LW263_S3_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6673PFDE/",
"accession": "IGVFFI6673PFDE",
"aliases": [
"gary-hon:LW263_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:54:10.484955+00:00",
"file_format": "fastq",
"file_size": 447603132,
"href": "/sequence-files/IGVFFI6673PFDE/@@download/IGVFFI6673PFDE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/3714e32e-ed5c-434d-ae95-4b67696c7192/IGVFFI6673PFDE.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/LW263_S3_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3950HPMX/",
"accession": "IGVFFI3950HPMX",
"aliases": [
"gary-hon:LW263_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:54:18.626567+00:00",
"file_format": "fastq",
"file_size": 423153296,
"href": "/sequence-files/IGVFFI3950HPMX/@@download/IGVFFI3950HPMX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/0c0587e8-706a-41c6-be92-59cc82495194/IGVFFI3950HPMX.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5242ONUU/",
"accession": "IGVFFI5242ONUU",
"aliases": [
"gary-hon:LW263_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:54:42.345710+00:00",
"file_format": "fastq",
"file_size": 3461324309,
"href": "/sequence-files/IGVFFI5242ONUU/@@download/IGVFFI5242ONUU.fastq.gz",
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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/LW263_S3_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9286IOQJ/",
"accession": "IGVFFI9286IOQJ",
"aliases": [
"gary-hon:LW263_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:54:26.382307+00:00",
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
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"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/IGVFSM0333RWYR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0333RWYR",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW263"
],
"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_LW263), 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": "2024-02-20T17:52:59.793968+00:00",
"submitter_comment": "Transcriptiome for LW263'",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "16d2bf43-4efb-434f-8f46-24e2fd65e76d"
}