{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4088YJYC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4088YJYC",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW267"
],
"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": "Measurement set [IGVFDS4088YJYC](/measurement-sets/IGVFDS4088YJYC/) has sequence file(s) [IGVFFI0415MIPE](/sequence-files/IGVFFI0415MIPE/), [IGVFFI0951POCE](/sequence-files/IGVFFI0951POCE/), [IGVFFI0284OSPU](/sequence-files/IGVFFI0284OSPU/), [IGVFFI1966VQPY](/sequence-files/IGVFFI1966VQPY/), [IGVFFI4437LLII](/sequence-files/IGVFFI4437LLII/), [IGVFFI2816YSZC](/sequence-files/IGVFFI2816YSZC/), [IGVFFI0167NBMB](/sequence-files/IGVFFI0167NBMB/), [IGVFFI9486ITWD](/sequence-files/IGVFFI9486ITWD/) 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/IGVFDS4088YJYC/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4088YJYC](/measurement-sets/IGVFDS4088YJYC/) has sequence file(s): [IGVFFI0415MIPE](/sequence-files/IGVFFI0415MIPE/), [IGVFFI0951POCE](/sequence-files/IGVFFI0951POCE/), [IGVFFI0284OSPU](/sequence-files/IGVFFI0284OSPU/), [IGVFFI1966VQPY](/sequence-files/IGVFFI1966VQPY/), [IGVFFI4437LLII](/sequence-files/IGVFFI4437LLII/), [IGVFFI2816YSZC](/sequence-files/IGVFFI2816YSZC/), [IGVFFI0167NBMB](/sequence-files/IGVFFI0167NBMB/), [IGVFFI9486ITWD](/sequence-files/IGVFFI9486ITWD/) 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/IGVFDS4088YJYC/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8445PWTI](/auxiliary-sets/IGVFDS8445PWTI/) has sequence file(s) [IGVFFI2720EZVT](/sequence-files/IGVFFI2720EZVT/), [IGVFFI7940PMVL](/sequence-files/IGVFFI7940PMVL/), [IGVFFI1918RPKD](/sequence-files/IGVFFI1918RPKD/), [IGVFFI4208OCGQ](/sequence-files/IGVFFI4208OCGQ/) 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/IGVFDS8445PWTI/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8445PWTI](/auxiliary-sets/IGVFDS8445PWTI/) has sequence file(s): [IGVFFI2720EZVT](/sequence-files/IGVFFI2720EZVT/), [IGVFFI7940PMVL](/sequence-files/IGVFFI7940PMVL/), [IGVFFI1918RPKD](/sequence-files/IGVFFI1918RPKD/), [IGVFFI4208OCGQ](/sequence-files/IGVFFI4208OCGQ/) 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/IGVFDS8445PWTI/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6787YPNQ](/auxiliary-sets/IGVFDS6787YPNQ/) has sequence file(s) [IGVFFI7677YUQR](/sequence-files/IGVFFI7677YUQR/), [IGVFFI9760OIHQ](/sequence-files/IGVFFI9760OIHQ/), [IGVFFI3213XORW](/sequence-files/IGVFFI3213XORW/), [IGVFFI7835NCQX](/sequence-files/IGVFFI7835NCQX/) 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/IGVFDS6787YPNQ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6787YPNQ](/auxiliary-sets/IGVFDS6787YPNQ/) has sequence file(s): [IGVFFI7677YUQR](/sequence-files/IGVFFI7677YUQR/), [IGVFFI9760OIHQ](/sequence-files/IGVFFI9760OIHQ/), [IGVFFI3213XORW](/sequence-files/IGVFFI3213XORW/), [IGVFFI7835NCQX](/sequence-files/IGVFFI7835NCQX/) 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/IGVFDS6787YPNQ/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8445PWTI/",
"accession": "IGVFDS8445PWTI",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW267"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6787YPNQ/",
"accession": "IGVFDS6787YPNQ",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW267"
],
"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": "2024-02-15T23:43:27.142504+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/IGVFFI0415MIPE/",
"accession": "IGVFFI0415MIPE",
"aliases": [
"gary-hon:LW267_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:03:09.078135+00:00",
"file_format": "fastq",
"file_size": 1667345818,
"href": "/sequence-files/IGVFFI0415MIPE/@@download/IGVFFI0415MIPE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/fc28034a-0d1e-44ee-bc2b-f1eecf48b7c0/IGVFFI0415MIPE.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/LW267_S7_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0951POCE/",
"accession": "IGVFFI0951POCE",
"aliases": [
"gary-hon:LW267_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:04:07.148050+00:00",
"file_format": "fastq",
"file_size": 512056540,
"href": "/sequence-files/IGVFFI0951POCE/@@download/IGVFFI0951POCE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/be553b56-6c40-4209-8af9-0e8af8e71262/IGVFFI0951POCE.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/LW267_S7_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0284OSPU/",
"accession": "IGVFFI0284OSPU",
"aliases": [
"gary-hon:LW267_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:04:41.900866+00:00",
"file_format": "fastq",
"file_size": 3846359718,
"href": "/sequence-files/IGVFFI0284OSPU/@@download/IGVFFI0284OSPU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/5d01bd15-5d9f-49fd-94b2-26f1c5918925/IGVFFI0284OSPU.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/LW267_S7_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1966VQPY/",
"accession": "IGVFFI1966VQPY",
"aliases": [
"gary-hon:LW267_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:04:15.842951+00:00",
"file_format": "fastq",
"file_size": 487502830,
"href": "/sequence-files/IGVFFI1966VQPY/@@download/IGVFFI1966VQPY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/028e24d0-2a21-444f-934e-d8579bec3e56/IGVFFI1966VQPY.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/LW267_S7_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4437LLII/",
"accession": "IGVFFI4437LLII",
"aliases": [
"gary-hon:LW267_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:04:24.488785+00:00",
"file_format": "fastq",
"file_size": 1530110893,
"href": "/sequence-files/IGVFFI4437LLII/@@download/IGVFFI4437LLII.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/bad35d07-a186-43c6-b8f8-3bb7654c59c1/IGVFFI4437LLII.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/LW267_S7_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2816YSZC/",
"accession": "IGVFFI2816YSZC",
"aliases": [
"gary-hon:LW267_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:03:27.788463+00:00",
"file_format": "fastq",
"file_size": 4104345122,
"href": "/sequence-files/IGVFFI2816YSZC/@@download/IGVFFI2816YSZC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/45f2909d-908a-4734-b9e5-1bc40be2a110/IGVFFI2816YSZC.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/LW267_S7_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0167NBMB/",
"accession": "IGVFFI0167NBMB",
"aliases": [
"gary-hon:LW267_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:03:00.151069+00:00",
"file_format": "fastq",
"file_size": 529488595,
"href": "/sequence-files/IGVFFI0167NBMB/@@download/IGVFFI0167NBMB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/a12c333a-6b00-4657-b1b3-f486c93313cf/IGVFFI0167NBMB.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/LW267_S7_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9486ITWD/",
"accession": "IGVFFI9486ITWD",
"aliases": [
"gary-hon:LW267_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:02:50.896615+00:00",
"file_format": "fastq",
"file_size": 563875125,
"href": "/sequence-files/IGVFFI9486ITWD/@@download/IGVFFI9486ITWD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/1cf79026-274f-4727-adf1-37ed379fa03f/IGVFFI9486ITWD.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/LW267_S7_L001_I1_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/IGVFSM5628VVVG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5628VVVG",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW267"
],
"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_LW267), 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": "2024-02-20T18:02:50.896615+00:00",
"submitter_comment": "Transcriptiome for LW267'",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "a860413b-261a-4705-a9e6-6ee8309c80aa"
}