{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8810ABUD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8810ABUD",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_LW282"
],
"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 [IGVFDS8810ABUD](/measurement-sets/IGVFDS8810ABUD/) has sequence file(s) [IGVFFI5962SCOE](/sequence-files/IGVFFI5962SCOE/), [IGVFFI0480OGUQ](/sequence-files/IGVFFI0480OGUQ/), [IGVFFI0724COUK](/sequence-files/IGVFFI0724COUK/), [IGVFFI6944QPBK](/sequence-files/IGVFFI6944QPBK/), [IGVFFI2488TFIW](/sequence-files/IGVFFI2488TFIW/), [IGVFFI5032ZZGX](/sequence-files/IGVFFI5032ZZGX/), [IGVFFI6517QDFT](/sequence-files/IGVFFI6517QDFT/), [IGVFFI9269XLGJ](/sequence-files/IGVFFI9269XLGJ/) 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/IGVFDS8810ABUD/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8810ABUD](/measurement-sets/IGVFDS8810ABUD/) has sequence file(s): [IGVFFI5962SCOE](/sequence-files/IGVFFI5962SCOE/), [IGVFFI0480OGUQ](/sequence-files/IGVFFI0480OGUQ/), [IGVFFI0724COUK](/sequence-files/IGVFFI0724COUK/), [IGVFFI6944QPBK](/sequence-files/IGVFFI6944QPBK/), [IGVFFI2488TFIW](/sequence-files/IGVFFI2488TFIW/), [IGVFFI5032ZZGX](/sequence-files/IGVFFI5032ZZGX/), [IGVFFI6517QDFT](/sequence-files/IGVFFI6517QDFT/), [IGVFFI9269XLGJ](/sequence-files/IGVFFI9269XLGJ/) 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/IGVFDS8810ABUD/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7986GKWR](/auxiliary-sets/IGVFDS7986GKWR/) has sequence file(s) [IGVFFI9536AHMJ](/sequence-files/IGVFFI9536AHMJ/), [IGVFFI2700GHXT](/sequence-files/IGVFFI2700GHXT/), [IGVFFI9141KKTA](/sequence-files/IGVFFI9141KKTA/), [IGVFFI3164PDJY](/sequence-files/IGVFFI3164PDJY/), [IGVFFI3852EJBS](/sequence-files/IGVFFI3852EJBS/), [IGVFFI3491WALI](/sequence-files/IGVFFI3491WALI/), [IGVFFI2014MVWI](/sequence-files/IGVFFI2014MVWI/), [IGVFFI3418CTXX](/sequence-files/IGVFFI3418CTXX/) 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/IGVFDS7986GKWR/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7986GKWR](/auxiliary-sets/IGVFDS7986GKWR/) has sequence file(s): [IGVFFI9536AHMJ](/sequence-files/IGVFFI9536AHMJ/), [IGVFFI2700GHXT](/sequence-files/IGVFFI2700GHXT/), [IGVFFI9141KKTA](/sequence-files/IGVFFI9141KKTA/), [IGVFFI3164PDJY](/sequence-files/IGVFFI3164PDJY/), [IGVFFI3852EJBS](/sequence-files/IGVFFI3852EJBS/), [IGVFFI3491WALI](/sequence-files/IGVFFI3491WALI/), [IGVFFI2014MVWI](/sequence-files/IGVFFI2014MVWI/), [IGVFFI3418CTXX](/sequence-files/IGVFFI3418CTXX/) 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/IGVFDS7986GKWR/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3567LQMB](/auxiliary-sets/IGVFDS3567LQMB/) has sequence file(s) [IGVFFI1692PBQW](/sequence-files/IGVFFI1692PBQW/), [IGVFFI5482BVUW](/sequence-files/IGVFFI5482BVUW/), [IGVFFI9298IPBX](/sequence-files/IGVFFI9298IPBX/), [IGVFFI0409KOWK](/sequence-files/IGVFFI0409KOWK/), [IGVFFI3785WYDT](/sequence-files/IGVFFI3785WYDT/), [IGVFFI5436EVPV](/sequence-files/IGVFFI5436EVPV/), [IGVFFI2912RLLI](/sequence-files/IGVFFI2912RLLI/), [IGVFFI4099YBZW](/sequence-files/IGVFFI4099YBZW/) 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/IGVFDS3567LQMB/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3567LQMB](/auxiliary-sets/IGVFDS3567LQMB/) has sequence file(s): [IGVFFI1692PBQW](/sequence-files/IGVFFI1692PBQW/), [IGVFFI5482BVUW](/sequence-files/IGVFFI5482BVUW/), [IGVFFI9298IPBX](/sequence-files/IGVFFI9298IPBX/), [IGVFFI0409KOWK](/sequence-files/IGVFFI0409KOWK/), [IGVFFI3785WYDT](/sequence-files/IGVFFI3785WYDT/), [IGVFFI5436EVPV](/sequence-files/IGVFFI5436EVPV/), [IGVFFI2912RLLI](/sequence-files/IGVFFI2912RLLI/), [IGVFFI4099YBZW](/sequence-files/IGVFFI4099YBZW/) 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/IGVFDS3567LQMB/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7986GKWR/",
"accession": "IGVFDS7986GKWR",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_sgRNA_LW282"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3567LQMB/",
"accession": "IGVFDS3567LQMB",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_NPC_HTO_LW282"
],
"file_set_type": "cell hashing barcode 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": "2024-02-29T16:52:22.949040+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/IGVFFI5962SCOE/",
"accession": "IGVFFI5962SCOE",
"aliases": [
"gary-hon:LW282_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:20:32.454723+00:00",
"file_format": "fastq",
"file_size": 122064232,
"href": "/sequence-files/IGVFFI5962SCOE/@@download/IGVFFI5962SCOE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/2fc298a1-ee2c-4afd-a5ac-7c6d1d7583e7/IGVFFI5962SCOE.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282_S20_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0480OGUQ/",
"accession": "IGVFFI0480OGUQ",
"aliases": [
"gary-hon:LW282_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:21:16.939592+00:00",
"file_format": "fastq",
"file_size": 304514898,
"href": "/sequence-files/IGVFFI0480OGUQ/@@download/IGVFFI0480OGUQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/5c153d08-0f9c-4823-89af-a9a5f76c3135/IGVFFI0480OGUQ.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282_S20_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0724COUK/",
"accession": "IGVFFI0724COUK",
"aliases": [
"gary-hon:LW282_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:20:52.491254+00:00",
"file_format": "fastq",
"file_size": 731632297,
"href": "/sequence-files/IGVFFI0724COUK/@@download/IGVFFI0724COUK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/67273e74-4f7e-4861-81f0-41618e1144ed/IGVFFI0724COUK.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282_S20_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6944QPBK/",
"accession": "IGVFFI6944QPBK",
"aliases": [
"gary-hon:LW282_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:21:02.657642+00:00",
"file_format": "fastq",
"file_size": 120960878,
"href": "/sequence-files/IGVFFI6944QPBK/@@download/IGVFFI6944QPBK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/a249ac07-05b0-41f4-9f62-28884ef1b18d/IGVFFI6944QPBK.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282_S20_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2488TFIW/",
"accession": "IGVFFI2488TFIW",
"aliases": [
"gary-hon:LW282_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:20:46.000947+00:00",
"file_format": "fastq",
"file_size": 310580740,
"href": "/sequence-files/IGVFFI2488TFIW/@@download/IGVFFI2488TFIW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/6467d187-9917-4b08-b99f-4c2f3350222c/IGVFFI2488TFIW.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282_S20_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5032ZZGX/",
"accession": "IGVFFI5032ZZGX",
"aliases": [
"gary-hon:LW282_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:21:12.402547+00:00",
"file_format": "fastq",
"file_size": 98099201,
"href": "/sequence-files/IGVFFI5032ZZGX/@@download/IGVFFI5032ZZGX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/c8225eab-d55b-454f-9801-2189ea914e3a/IGVFFI5032ZZGX.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282_S20_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6517QDFT/",
"accession": "IGVFFI6517QDFT",
"aliases": [
"gary-hon:LW282_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:20:40.962973+00:00",
"file_format": "fastq",
"file_size": 101970876,
"href": "/sequence-files/IGVFFI6517QDFT/@@download/IGVFFI6517QDFT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/bff287f1-b598-4599-8e75-0dba5af0864c/IGVFFI6517QDFT.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282_S20_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9269XLGJ/",
"accession": "IGVFFI9269XLGJ",
"aliases": [
"gary-hon:LW282_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:21:28.430862+00:00",
"file_format": "fastq",
"file_size": 713673212,
"href": "/sequence-files/IGVFFI9269XLGJ/@@download/IGVFFI9269XLGJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/98b5eaef-6d08-4a31-b3a2-7af627921a24/IGVFFI9269XLGJ.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/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW282_S20_L002_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1588TVKF/"
],
"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/IGVFSM1288TQKF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1288TQKF",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW282"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2302LCEO/",
"accession": "IGVFDS2302LCEO",
"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 neural stem cell for 20 days (cellular sub pool: subpool_LW282), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000047/",
"status": "preview",
"term_name": "neural stem cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-03-01T17:18:46.886742+00:00",
"submitter_comment": "Transcriptiome for LW282",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "72de59a0-1f71-4b6b-a0eb-6f062c62afc4"
}