{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5173WYKU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5173WYKU",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW268"
],
"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 [IGVFDS5031XGGB](/auxiliary-sets/IGVFDS5031XGGB/) has sequence file(s) [IGVFFI5384GZHX](/sequence-files/IGVFFI5384GZHX/), [IGVFFI3916MOXA](/sequence-files/IGVFFI3916MOXA/), [IGVFFI2756EFLJ](/sequence-files/IGVFFI2756EFLJ/), [IGVFFI3594VEZZ](/sequence-files/IGVFFI3594VEZZ/) 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/IGVFDS5031XGGB/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5031XGGB](/auxiliary-sets/IGVFDS5031XGGB/) has sequence file(s): [IGVFFI5384GZHX](/sequence-files/IGVFFI5384GZHX/), [IGVFFI3916MOXA](/sequence-files/IGVFFI3916MOXA/), [IGVFFI2756EFLJ](/sequence-files/IGVFFI2756EFLJ/), [IGVFFI3594VEZZ](/sequence-files/IGVFFI3594VEZZ/) 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/IGVFDS5031XGGB/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3625MSZP](/auxiliary-sets/IGVFDS3625MSZP/) has sequence file(s) [IGVFFI3144NXDU](/sequence-files/IGVFFI3144NXDU/), [IGVFFI5357FGJY](/sequence-files/IGVFFI5357FGJY/), [IGVFFI4477BFFF](/sequence-files/IGVFFI4477BFFF/), [IGVFFI7018AWNR](/sequence-files/IGVFFI7018AWNR/) 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/IGVFDS3625MSZP/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3625MSZP](/auxiliary-sets/IGVFDS3625MSZP/) has sequence file(s): [IGVFFI3144NXDU](/sequence-files/IGVFFI3144NXDU/), [IGVFFI5357FGJY](/sequence-files/IGVFFI5357FGJY/), [IGVFFI4477BFFF](/sequence-files/IGVFFI4477BFFF/), [IGVFFI7018AWNR](/sequence-files/IGVFFI7018AWNR/) 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/IGVFDS3625MSZP/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5173WYKU](/measurement-sets/IGVFDS5173WYKU/) has sequence file(s) [IGVFFI3911AOPY](/sequence-files/IGVFFI3911AOPY/), [IGVFFI2744VQUN](/sequence-files/IGVFFI2744VQUN/), [IGVFFI5159VBLC](/sequence-files/IGVFFI5159VBLC/), [IGVFFI0771ABVH](/sequence-files/IGVFFI0771ABVH/), [IGVFFI9820XEVN](/sequence-files/IGVFFI9820XEVN/), [IGVFFI1214OHMN](/sequence-files/IGVFFI1214OHMN/), [IGVFFI9051VUTG](/sequence-files/IGVFFI9051VUTG/), [IGVFFI4843TPYK](/sequence-files/IGVFFI4843TPYK/) 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/IGVFDS5173WYKU/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5173WYKU](/measurement-sets/IGVFDS5173WYKU/) has sequence file(s): [IGVFFI3911AOPY](/sequence-files/IGVFFI3911AOPY/), [IGVFFI2744VQUN](/sequence-files/IGVFFI2744VQUN/), [IGVFFI5159VBLC](/sequence-files/IGVFFI5159VBLC/), [IGVFFI0771ABVH](/sequence-files/IGVFFI0771ABVH/), [IGVFFI9820XEVN](/sequence-files/IGVFFI9820XEVN/), [IGVFFI1214OHMN](/sequence-files/IGVFFI1214OHMN/), [IGVFFI9051VUTG](/sequence-files/IGVFFI9051VUTG/), [IGVFFI4843TPYK](/sequence-files/IGVFFI4843TPYK/) 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/IGVFDS5173WYKU/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS3625MSZP/",
"accession": "IGVFDS3625MSZP",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW268"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS5031XGGB/",
"accession": "IGVFDS5031XGGB",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW268"
],
"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": "2024-02-15T23:43:28.302644+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/IGVFFI3911AOPY/",
"accession": "IGVFFI3911AOPY",
"aliases": [
"gary-hon:LW268_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:06:52.789266+00:00",
"file_format": "fastq",
"file_size": 1560812475,
"href": "/sequence-files/IGVFFI3911AOPY/@@download/IGVFFI3911AOPY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/c0a85b2c-301a-4d80-bf0e-c8f61c0cbbf0/IGVFFI3911AOPY.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/LW268_S8_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2744VQUN/",
"accession": "IGVFFI2744VQUN",
"aliases": [
"gary-hon:LW268_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:05:27.747672+00:00",
"file_format": "fastq",
"file_size": 578912710,
"href": "/sequence-files/IGVFFI2744VQUN/@@download/IGVFFI2744VQUN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/e0fd15f6-9194-4019-87d9-9cca0b343f64/IGVFFI2744VQUN.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/LW268_S8_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5159VBLC/",
"accession": "IGVFFI5159VBLC",
"aliases": [
"gary-hon:LW268_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:05:55.557929+00:00",
"file_format": "fastq",
"file_size": 4123769133,
"href": "/sequence-files/IGVFFI5159VBLC/@@download/IGVFFI5159VBLC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/4f1cba08-71a5-4677-bb56-db7898619d04/IGVFFI5159VBLC.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/LW268_S8_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0771ABVH/",
"accession": "IGVFFI0771ABVH",
"aliases": [
"gary-hon:LW268_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:06:44.014923+00:00",
"file_format": "fastq",
"file_size": 521286304,
"href": "/sequence-files/IGVFFI0771ABVH/@@download/IGVFFI0771ABVH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/1becc719-2533-4da8-85b8-50c3b57368e3/IGVFFI0771ABVH.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/LW268_S8_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9820XEVN/",
"accession": "IGVFFI9820XEVN",
"aliases": [
"gary-hon:LW268_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:05:18.904169+00:00",
"file_format": "fastq",
"file_size": 517208071,
"href": "/sequence-files/IGVFFI9820XEVN/@@download/IGVFFI9820XEVN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/16b98bd5-222c-4bf9-abc3-dec651ef857b/IGVFFI9820XEVN.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/LW268_S8_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1214OHMN/",
"accession": "IGVFFI1214OHMN",
"aliases": [
"gary-hon:LW268_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:06:35.310011+00:00",
"file_format": "fastq",
"file_size": 472542855,
"href": "/sequence-files/IGVFFI1214OHMN/@@download/IGVFFI1214OHMN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/c0a4492a-37ac-4d79-8314-7b7327047481/IGVFFI1214OHMN.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/LW268_S8_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9051VUTG/",
"accession": "IGVFFI9051VUTG",
"aliases": [
"gary-hon:LW268_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:07:10.188705+00:00",
"file_format": "fastq",
"file_size": 3946832028,
"href": "/sequence-files/IGVFFI9051VUTG/@@download/IGVFFI9051VUTG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/b089e028-a4cf-4096-8ee5-44ea1330fcac/IGVFFI9051VUTG.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/LW268_S8_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4843TPYK/",
"accession": "IGVFFI4843TPYK",
"aliases": [
"gary-hon:LW268_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T18:05:37.216357+00:00",
"file_format": "fastq",
"file_size": 1664720538,
"href": "/sequence-files/IGVFFI4843TPYK/@@download/IGVFFI4843TPYK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/db0bb4ec-5e56-4ecb-9cb7-d8f0604e1920/IGVFFI4843TPYK.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/LW268_S8_L001_R1_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/IGVFSM2215YBLM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2215YBLM",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW268"
],
"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_LW268), 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": "2024-02-20T18:05:18.904169+00:00",
"submitter_comment": "Transcriptiome for LW268'",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "68b15f9e-837b-4c83-8907-eb0f0e6068f3"
}