{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5931MYJN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5931MYJN",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW266"
],
"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 [IGVFDS5931MYJN](/measurement-sets/IGVFDS5931MYJN/) has sequence file(s) [IGVFFI3699NCKX](/sequence-files/IGVFFI3699NCKX/), [IGVFFI3642MWTS](/sequence-files/IGVFFI3642MWTS/), [IGVFFI8404FJNJ](/sequence-files/IGVFFI8404FJNJ/), [IGVFFI7291HRWW](/sequence-files/IGVFFI7291HRWW/), [IGVFFI8529FWOJ](/sequence-files/IGVFFI8529FWOJ/), [IGVFFI3491XAHR](/sequence-files/IGVFFI3491XAHR/), [IGVFFI4944IHCL](/sequence-files/IGVFFI4944IHCL/), [IGVFFI4338NFLG](/sequence-files/IGVFFI4338NFLG/) 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/IGVFDS5931MYJN/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5931MYJN](/measurement-sets/IGVFDS5931MYJN/) has sequence file(s): [IGVFFI3699NCKX](/sequence-files/IGVFFI3699NCKX/), [IGVFFI3642MWTS](/sequence-files/IGVFFI3642MWTS/), [IGVFFI8404FJNJ](/sequence-files/IGVFFI8404FJNJ/), [IGVFFI7291HRWW](/sequence-files/IGVFFI7291HRWW/), [IGVFFI8529FWOJ](/sequence-files/IGVFFI8529FWOJ/), [IGVFFI3491XAHR](/sequence-files/IGVFFI3491XAHR/), [IGVFFI4944IHCL](/sequence-files/IGVFFI4944IHCL/), [IGVFFI4338NFLG](/sequence-files/IGVFFI4338NFLG/) 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/IGVFDS5931MYJN/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8001EMIV](/auxiliary-sets/IGVFDS8001EMIV/) has sequence file(s) [IGVFFI2828PDNY](/sequence-files/IGVFFI2828PDNY/), [IGVFFI9244QRVR](/sequence-files/IGVFFI9244QRVR/), [IGVFFI5054QLBL](/sequence-files/IGVFFI5054QLBL/), [IGVFFI2658YFUQ](/sequence-files/IGVFFI2658YFUQ/) 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/IGVFDS8001EMIV/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8001EMIV](/auxiliary-sets/IGVFDS8001EMIV/) has sequence file(s): [IGVFFI2828PDNY](/sequence-files/IGVFFI2828PDNY/), [IGVFFI9244QRVR](/sequence-files/IGVFFI9244QRVR/), [IGVFFI5054QLBL](/sequence-files/IGVFFI5054QLBL/), [IGVFFI2658YFUQ](/sequence-files/IGVFFI2658YFUQ/) 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/IGVFDS8001EMIV/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7944GWTS](/auxiliary-sets/IGVFDS7944GWTS/) has sequence file(s) [IGVFFI9006RKCZ](/sequence-files/IGVFFI9006RKCZ/), [IGVFFI0638VNPV](/sequence-files/IGVFFI0638VNPV/), [IGVFFI3275XOUB](/sequence-files/IGVFFI3275XOUB/), [IGVFFI2007EPSH](/sequence-files/IGVFFI2007EPSH/) 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/IGVFDS7944GWTS/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7944GWTS](/auxiliary-sets/IGVFDS7944GWTS/) has sequence file(s): [IGVFFI9006RKCZ](/sequence-files/IGVFFI9006RKCZ/), [IGVFFI0638VNPV](/sequence-files/IGVFFI0638VNPV/), [IGVFFI3275XOUB](/sequence-files/IGVFFI3275XOUB/), [IGVFFI2007EPSH](/sequence-files/IGVFFI2007EPSH/) 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/IGVFDS7944GWTS/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8001EMIV/",
"accession": "IGVFDS8001EMIV",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW266"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7944GWTS/",
"accession": "IGVFDS7944GWTS",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW266"
],
"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": "2024-02-15T23:43:26.118162+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/IGVFFI3699NCKX/",
"accession": "IGVFFI3699NCKX",
"aliases": [
"gary-hon:LW266_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:00:41.583734+00:00",
"file_format": "fastq",
"file_size": 1673459670,
"href": "/sequence-files/IGVFFI3699NCKX/@@download/IGVFFI3699NCKX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/af4dedc2-2da5-4001-b9e8-a64071368a4e/IGVFFI3699NCKX.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/LW266_S6_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3642MWTS/",
"accession": "IGVFFI3642MWTS",
"aliases": [
"gary-hon:LW266_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:01:39.485752+00:00",
"file_format": "fastq",
"file_size": 473711837,
"href": "/sequence-files/IGVFFI3642MWTS/@@download/IGVFFI3642MWTS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/9dc74fcf-94cf-4522-8e5d-e7243791470d/IGVFFI3642MWTS.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/LW266_S6_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8404FJNJ/",
"accession": "IGVFFI8404FJNJ",
"aliases": [
"gary-hon:LW266_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:01:56.688256+00:00",
"file_format": "fastq",
"file_size": 1532550960,
"href": "/sequence-files/IGVFFI8404FJNJ/@@download/IGVFFI8404FJNJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/b381cbf3-870c-4d7f-a994-098dbe718bc2/IGVFFI8404FJNJ.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/LW266_S6_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7291HRWW/",
"accession": "IGVFFI7291HRWW",
"aliases": [
"gary-hon:LW266_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:02:13.666446+00:00",
"file_format": "fastq",
"file_size": 3870919877,
"href": "/sequence-files/IGVFFI7291HRWW/@@download/IGVFFI7291HRWW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/ee8522ef-d5ea-4ba4-93ad-9ab4e35ba5a5/IGVFFI7291HRWW.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/LW266_S6_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8529FWOJ/",
"accession": "IGVFFI8529FWOJ",
"aliases": [
"gary-hon:LW266_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:00:32.561494+00:00",
"file_format": "fastq",
"file_size": 562451583,
"href": "/sequence-files/IGVFFI8529FWOJ/@@download/IGVFFI8529FWOJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/5675947d-14b1-4e0f-8431-d22da341a85b/IGVFFI8529FWOJ.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/LW266_S6_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3491XAHR/",
"accession": "IGVFFI3491XAHR",
"aliases": [
"gary-hon:LW266_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:01:47.863514+00:00",
"file_format": "fastq",
"file_size": 500697055,
"href": "/sequence-files/IGVFFI3491XAHR/@@download/IGVFFI3491XAHR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/d2cd4b75-c539-4f16-9f95-aa05006de924/IGVFFI3491XAHR.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/LW266_S6_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4944IHCL/",
"accession": "IGVFFI4944IHCL",
"aliases": [
"gary-hon:LW266_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:00:19.062269+00:00",
"file_format": "fastq",
"file_size": 523504998,
"href": "/sequence-files/IGVFFI4944IHCL/@@download/IGVFFI4944IHCL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/4397e728-551e-4346-afbb-a9b8852fb069/IGVFFI4944IHCL.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/LW266_S6_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4338NFLG/",
"accession": "IGVFFI4338NFLG",
"aliases": [
"gary-hon:LW266_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:01:00.254106+00:00",
"file_format": "fastq",
"file_size": 4140010459,
"href": "/sequence-files/IGVFFI4338NFLG/@@download/IGVFFI4338NFLG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/f0bbd75e-0c3b-497f-ab09-446873723c39/IGVFFI4338NFLG.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/LW266_S6_L001_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/IGVFSM4930FDUF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4930FDUF",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW266"
],
"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_LW266), 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": "2024-02-20T18:00:19.062269+00:00",
"submitter_comment": "Transcriptiome for LW266'",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "5da69cc0-f9db-46a7-a096-2ca8601c9401"
}