{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6054GEKL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6054GEKL",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW264"
],
"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 [IGVFDS3533NRTW](/auxiliary-sets/IGVFDS3533NRTW/) has sequence file(s) [IGVFFI2147OLQC](/sequence-files/IGVFFI2147OLQC/), [IGVFFI8172KHSP](/sequence-files/IGVFFI8172KHSP/), [IGVFFI9339EFZQ](/sequence-files/IGVFFI9339EFZQ/), [IGVFFI2974UJYR](/sequence-files/IGVFFI2974UJYR/) 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/IGVFDS3533NRTW/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3533NRTW](/auxiliary-sets/IGVFDS3533NRTW/) has sequence file(s): [IGVFFI2147OLQC](/sequence-files/IGVFFI2147OLQC/), [IGVFFI8172KHSP](/sequence-files/IGVFFI8172KHSP/), [IGVFFI9339EFZQ](/sequence-files/IGVFFI9339EFZQ/), [IGVFFI2974UJYR](/sequence-files/IGVFFI2974UJYR/) 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/IGVFDS3533NRTW/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS4926IAGY](/auxiliary-sets/IGVFDS4926IAGY/) has sequence file(s) [IGVFFI5091VQUO](/sequence-files/IGVFFI5091VQUO/), [IGVFFI9705OPKD](/sequence-files/IGVFFI9705OPKD/), [IGVFFI9390TIHO](/sequence-files/IGVFFI9390TIHO/), [IGVFFI3694DSSY](/sequence-files/IGVFFI3694DSSY/) 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/IGVFDS4926IAGY/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4926IAGY](/auxiliary-sets/IGVFDS4926IAGY/) has sequence file(s): [IGVFFI5091VQUO](/sequence-files/IGVFFI5091VQUO/), [IGVFFI9705OPKD](/sequence-files/IGVFFI9705OPKD/), [IGVFFI9390TIHO](/sequence-files/IGVFFI9390TIHO/), [IGVFFI3694DSSY](/sequence-files/IGVFFI3694DSSY/) 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/IGVFDS4926IAGY/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS6054GEKL](/measurement-sets/IGVFDS6054GEKL/) has sequence file(s) [IGVFFI0832KEPC](/sequence-files/IGVFFI0832KEPC/), [IGVFFI3005ICNR](/sequence-files/IGVFFI3005ICNR/), [IGVFFI6995CWOO](/sequence-files/IGVFFI6995CWOO/), [IGVFFI1648TSYB](/sequence-files/IGVFFI1648TSYB/), [IGVFFI5883BJSS](/sequence-files/IGVFFI5883BJSS/), [IGVFFI1664QUMY](/sequence-files/IGVFFI1664QUMY/), [IGVFFI8141LWAA](/sequence-files/IGVFFI8141LWAA/), [IGVFFI5887SCUI](/sequence-files/IGVFFI5887SCUI/) 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/IGVFDS6054GEKL/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6054GEKL](/measurement-sets/IGVFDS6054GEKL/) has sequence file(s): [IGVFFI0832KEPC](/sequence-files/IGVFFI0832KEPC/), [IGVFFI3005ICNR](/sequence-files/IGVFFI3005ICNR/), [IGVFFI6995CWOO](/sequence-files/IGVFFI6995CWOO/), [IGVFFI1648TSYB](/sequence-files/IGVFFI1648TSYB/), [IGVFFI5883BJSS](/sequence-files/IGVFFI5883BJSS/), [IGVFFI1664QUMY](/sequence-files/IGVFFI1664QUMY/), [IGVFFI8141LWAA](/sequence-files/IGVFFI8141LWAA/), [IGVFFI5887SCUI](/sequence-files/IGVFFI5887SCUI/) 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/IGVFDS6054GEKL/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4926IAGY/",
"accession": "IGVFDS4926IAGY",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW264"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3533NRTW/",
"accession": "IGVFDS3533NRTW",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_sgRNA_LW264"
],
"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": "2024-02-15T23:43:23.889970+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/IGVFFI0832KEPC/",
"accession": "IGVFFI0832KEPC",
"aliases": [
"gary-hon:LW264_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:56:28.336440+00:00",
"file_format": "fastq",
"file_size": 417181900,
"href": "/sequence-files/IGVFFI0832KEPC/@@download/IGVFFI0832KEPC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/b5c5d09e-a245-418e-b731-fab8dd068f9c/IGVFFI0832KEPC.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/LW264_S4_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3005ICNR/",
"accession": "IGVFFI3005ICNR",
"aliases": [
"gary-hon:LW264_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:56:59.914154+00:00",
"file_format": "fastq",
"file_size": 3455036767,
"href": "/sequence-files/IGVFFI3005ICNR/@@download/IGVFFI3005ICNR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/ebfd514b-b176-4ce5-8352-9b121088eba9/IGVFFI3005ICNR.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/LW264_S4_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6995CWOO/",
"accession": "IGVFFI6995CWOO",
"aliases": [
"gary-hon:LW264_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:55:52.799875+00:00",
"file_format": "fastq",
"file_size": 3685964399,
"href": "/sequence-files/IGVFFI6995CWOO/@@download/IGVFFI6995CWOO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/6c91636a-3acd-4042-8aca-bf3221c6e27b/IGVFFI6995CWOO.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/LW264_S4_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1648TSYB/",
"accession": "IGVFFI1648TSYB",
"aliases": [
"gary-hon:LW264_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:55:16.009937+00:00",
"file_format": "fastq",
"file_size": 451427783,
"href": "/sequence-files/IGVFFI1648TSYB/@@download/IGVFFI1648TSYB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/5b3d7946-3f43-4875-aa53-4ce8ed8139a7/IGVFFI1648TSYB.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/LW264_S4_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5883BJSS/",
"accession": "IGVFFI5883BJSS",
"aliases": [
"gary-hon:LW264_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:55:27.653706+00:00",
"file_format": "fastq",
"file_size": 436308416,
"href": "/sequence-files/IGVFFI5883BJSS/@@download/IGVFFI5883BJSS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/40ba72cd-d9e2-4969-a466-23d80a3f5d7a/IGVFFI5883BJSS.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/LW264_S4_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1664QUMY/",
"accession": "IGVFFI1664QUMY",
"aliases": [
"gary-hon:LW264_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:55:35.624649+00:00",
"file_format": "fastq",
"file_size": 1495286089,
"href": "/sequence-files/IGVFFI1664QUMY/@@download/IGVFFI1664QUMY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/feb70ad4-5529-4c46-88ec-924a108a95dc/IGVFFI1664QUMY.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/LW264_S4_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8141LWAA/",
"accession": "IGVFFI8141LWAA",
"aliases": [
"gary-hon:LW264_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:56:36.256702+00:00",
"file_format": "fastq",
"file_size": 402147296,
"href": "/sequence-files/IGVFFI8141LWAA/@@download/IGVFFI8141LWAA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/8fd79159-80e0-4d6c-b976-5a3ff3d7cc2a/IGVFFI8141LWAA.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/LW264_S4_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5887SCUI/",
"accession": "IGVFFI5887SCUI",
"aliases": [
"gary-hon:LW264_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T17:56:44.040728+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI5887SCUI/@@download/IGVFFI5887SCUI.fastq.gz",
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"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/LW264_S4_L002_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/IGVFSM0981UTUA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0981UTUA",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW264"
],
"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_LW264), 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": "2024-02-20T17:55:16.009937+00:00",
"submitter_comment": "Transcriptiome for LW264'",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "de5e46b9-d343-40f4-8725-6facd3ccabb5"
}