{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5033OBAO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5033OBAO",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW265"
],
"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 [IGVFDS5033OBAO](/measurement-sets/IGVFDS5033OBAO/) has sequence file(s) [IGVFFI5312MTPV](/sequence-files/IGVFFI5312MTPV/), [IGVFFI0514WTDY](/sequence-files/IGVFFI0514WTDY/), [IGVFFI7590TIFL](/sequence-files/IGVFFI7590TIFL/), [IGVFFI3835WKIZ](/sequence-files/IGVFFI3835WKIZ/), [IGVFFI8436EDEK](/sequence-files/IGVFFI8436EDEK/), [IGVFFI9055CJNY](/sequence-files/IGVFFI9055CJNY/), [IGVFFI9909EVUS](/sequence-files/IGVFFI9909EVUS/), [IGVFFI1034SQQC](/sequence-files/IGVFFI1034SQQC/) 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/IGVFDS5033OBAO/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5033OBAO](/measurement-sets/IGVFDS5033OBAO/) has sequence file(s): [IGVFFI5312MTPV](/sequence-files/IGVFFI5312MTPV/), [IGVFFI0514WTDY](/sequence-files/IGVFFI0514WTDY/), [IGVFFI7590TIFL](/sequence-files/IGVFFI7590TIFL/), [IGVFFI3835WKIZ](/sequence-files/IGVFFI3835WKIZ/), [IGVFFI8436EDEK](/sequence-files/IGVFFI8436EDEK/), [IGVFFI9055CJNY](/sequence-files/IGVFFI9055CJNY/), [IGVFFI9909EVUS](/sequence-files/IGVFFI9909EVUS/), [IGVFFI1034SQQC](/sequence-files/IGVFFI1034SQQC/) 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/IGVFDS5033OBAO/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3633OXMI](/auxiliary-sets/IGVFDS3633OXMI/) has sequence file(s) [IGVFFI6653WHJW](/sequence-files/IGVFFI6653WHJW/), [IGVFFI4629JAWT](/sequence-files/IGVFFI4629JAWT/), [IGVFFI9092WARW](/sequence-files/IGVFFI9092WARW/), [IGVFFI6791VIRM](/sequence-files/IGVFFI6791VIRM/) 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/IGVFDS3633OXMI/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3633OXMI](/auxiliary-sets/IGVFDS3633OXMI/) has sequence file(s): [IGVFFI6653WHJW](/sequence-files/IGVFFI6653WHJW/), [IGVFFI4629JAWT](/sequence-files/IGVFFI4629JAWT/), [IGVFFI9092WARW](/sequence-files/IGVFFI9092WARW/), [IGVFFI6791VIRM](/sequence-files/IGVFFI6791VIRM/) 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/IGVFDS3633OXMI/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7126MOZN](/auxiliary-sets/IGVFDS7126MOZN/) has sequence file(s) [IGVFFI9073DXNX](/sequence-files/IGVFFI9073DXNX/), [IGVFFI4148SPYG](/sequence-files/IGVFFI4148SPYG/), [IGVFFI0764VODB](/sequence-files/IGVFFI0764VODB/), [IGVFFI2927WRJG](/sequence-files/IGVFFI2927WRJG/) 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/IGVFDS7126MOZN/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7126MOZN](/auxiliary-sets/IGVFDS7126MOZN/) has sequence file(s): [IGVFFI9073DXNX](/sequence-files/IGVFFI9073DXNX/), [IGVFFI4148SPYG](/sequence-files/IGVFFI4148SPYG/), [IGVFFI0764VODB](/sequence-files/IGVFFI0764VODB/), [IGVFFI2927WRJG](/sequence-files/IGVFFI2927WRJG/) 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/IGVFDS7126MOZN/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3633OXMI/",
"accession": "IGVFDS3633OXMI",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW265"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7126MOZN/",
"accession": "IGVFDS7126MOZN",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW265"
],
"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": "2024-02-15T23:43:24.898375+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/IGVFFI5312MTPV/",
"accession": "IGVFFI5312MTPV",
"aliases": [
"gary-hon:LW265_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:57:52.383323+00:00",
"file_format": "fastq",
"file_size": 1846827070,
"href": "/sequence-files/IGVFFI5312MTPV/@@download/IGVFFI5312MTPV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/9dc11a56-a199-4897-be23-c9adae74f772/IGVFFI5312MTPV.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/LW265_S5_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0514WTDY/",
"accession": "IGVFFI0514WTDY",
"aliases": [
"gary-hon:LW265_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:59:18.540863+00:00",
"file_format": "fastq",
"file_size": 1722033058,
"href": "/sequence-files/IGVFFI0514WTDY/@@download/IGVFFI0514WTDY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/64dbb133-7621-4d00-9735-9a02c6e686be/IGVFFI0514WTDY.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/LW265_S5_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7590TIFL/",
"accession": "IGVFFI7590TIFL",
"aliases": [
"gary-hon:LW265_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:58:12.238564+00:00",
"file_format": "fastq",
"file_size": 4581960740,
"href": "/sequence-files/IGVFFI7590TIFL/@@download/IGVFFI7590TIFL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/95cf687a-00de-47b6-9ca3-1d0ac1ed992a/IGVFFI7590TIFL.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/LW265_S5_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3835WKIZ/",
"accession": "IGVFFI3835WKIZ",
"aliases": [
"gary-hon:LW265_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:59:37.465795+00:00",
"file_format": "fastq",
"file_size": 4356626782,
"href": "/sequence-files/IGVFFI3835WKIZ/@@download/IGVFFI3835WKIZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/8dc1876b-a19b-4e7a-a8de-96a8f7498b54/IGVFFI3835WKIZ.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/LW265_S5_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8436EDEK/",
"accession": "IGVFFI8436EDEK",
"aliases": [
"gary-hon:LW265_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:58:56.722926+00:00",
"file_format": "fastq",
"file_size": 565122871,
"href": "/sequence-files/IGVFFI8436EDEK/@@download/IGVFFI8436EDEK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/77c55770-eb5e-4f50-8644-7af01a8a8433/IGVFFI8436EDEK.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/LW265_S5_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9055CJNY/",
"accession": "IGVFFI9055CJNY",
"aliases": [
"gary-hon:LW265_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:57:33.637951+00:00",
"file_format": "fastq",
"file_size": 587458313,
"href": "/sequence-files/IGVFFI9055CJNY/@@download/IGVFFI9055CJNY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/3570388e-8fe5-476e-9c82-6147cb8f95cb/IGVFFI9055CJNY.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/LW265_S5_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9909EVUS/",
"accession": "IGVFFI9909EVUS",
"aliases": [
"gary-hon:LW265_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:59:09.360358+00:00",
"file_format": "fastq",
"file_size": 566558677,
"href": "/sequence-files/IGVFFI9909EVUS/@@download/IGVFFI9909EVUS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/88d7a06b-68f8-4e78-a1d9-11950de148f3/IGVFFI9909EVUS.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/LW265_S5_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1034SQQC/",
"accession": "IGVFFI1034SQQC",
"aliases": [
"gary-hon:LW265_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:57:43.030091+00:00",
"file_format": "fastq",
"file_size": 613602189,
"href": "/sequence-files/IGVFFI1034SQQC/@@download/IGVFFI1034SQQC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/d93abc07-064d-4bea-8ac0-7caefba9c26c/IGVFFI1034SQQC.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/LW265_S5_L001_I2_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/IGVFSM7215JDPM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7215JDPM",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW265"
],
"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_LW265), 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": "2024-02-20T17:57:33.637951+00:00",
"submitter_comment": "Transcriptiome for LW265'",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "7d999a47-35a2-4cff-8866-99dc93d29a8c"
}