{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3975OFAO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3975OFAO",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_LW288"
],
"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 [IGVFDS6503WNZT](/auxiliary-sets/IGVFDS6503WNZT/) has sequence file(s) [IGVFFI8822WNTR](/sequence-files/IGVFFI8822WNTR/), [IGVFFI9641ZDCL](/sequence-files/IGVFFI9641ZDCL/), [IGVFFI0507ZCWD](/sequence-files/IGVFFI0507ZCWD/), [IGVFFI8913KNGR](/sequence-files/IGVFFI8913KNGR/) 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/IGVFDS6503WNZT/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6503WNZT](/auxiliary-sets/IGVFDS6503WNZT/) has sequence file(s): [IGVFFI8822WNTR](/sequence-files/IGVFFI8822WNTR/), [IGVFFI9641ZDCL](/sequence-files/IGVFFI9641ZDCL/), [IGVFFI0507ZCWD](/sequence-files/IGVFFI0507ZCWD/), [IGVFFI8913KNGR](/sequence-files/IGVFFI8913KNGR/) 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/IGVFDS6503WNZT/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3975OFAO](/measurement-sets/IGVFDS3975OFAO/) has sequence file(s) [IGVFFI9129JCPC](/sequence-files/IGVFFI9129JCPC/), [IGVFFI2364WFHK](/sequence-files/IGVFFI2364WFHK/), [IGVFFI2717TTOD](/sequence-files/IGVFFI2717TTOD/), [IGVFFI5124UFYH](/sequence-files/IGVFFI5124UFYH/), [IGVFFI1526NFSS](/sequence-files/IGVFFI1526NFSS/), [IGVFFI9278DMWO](/sequence-files/IGVFFI9278DMWO/), [IGVFFI5388NBDD](/sequence-files/IGVFFI5388NBDD/), [IGVFFI3403UWCY](/sequence-files/IGVFFI3403UWCY/) 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/IGVFDS3975OFAO/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3975OFAO](/measurement-sets/IGVFDS3975OFAO/) has sequence file(s): [IGVFFI9129JCPC](/sequence-files/IGVFFI9129JCPC/), [IGVFFI2364WFHK](/sequence-files/IGVFFI2364WFHK/), [IGVFFI2717TTOD](/sequence-files/IGVFFI2717TTOD/), [IGVFFI5124UFYH](/sequence-files/IGVFFI5124UFYH/), [IGVFFI1526NFSS](/sequence-files/IGVFFI1526NFSS/), [IGVFFI9278DMWO](/sequence-files/IGVFFI9278DMWO/), [IGVFFI5388NBDD](/sequence-files/IGVFFI5388NBDD/), [IGVFFI3403UWCY](/sequence-files/IGVFFI3403UWCY/) 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/IGVFDS3975OFAO/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9718OGWQ](/auxiliary-sets/IGVFDS9718OGWQ/) has sequence file(s) [IGVFFI4727MDMF](/sequence-files/IGVFFI4727MDMF/), [IGVFFI3517RBWJ](/sequence-files/IGVFFI3517RBWJ/), [IGVFFI1737ZJFQ](/sequence-files/IGVFFI1737ZJFQ/), [IGVFFI1799FWCW](/sequence-files/IGVFFI1799FWCW/) 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/IGVFDS9718OGWQ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9718OGWQ](/auxiliary-sets/IGVFDS9718OGWQ/) has sequence file(s): [IGVFFI4727MDMF](/sequence-files/IGVFFI4727MDMF/), [IGVFFI3517RBWJ](/sequence-files/IGVFFI3517RBWJ/), [IGVFFI1737ZJFQ](/sequence-files/IGVFFI1737ZJFQ/), [IGVFFI1799FWCW](/sequence-files/IGVFFI1799FWCW/) 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/IGVFDS9718OGWQ/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS6503WNZT/",
"accession": "IGVFDS6503WNZT",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_sgRNA_LW288"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS9718OGWQ/",
"accession": "IGVFDS9718OGWQ",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_HTO_LW288"
],
"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": "2024-02-21T21:28:51.977702+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/IGVFFI9129JCPC/",
"accession": "IGVFFI9129JCPC",
"aliases": [
"gary-hon:LW288_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:55:30.833750+00:00",
"file_format": "fastq",
"file_size": 777782261,
"href": "/sequence-files/IGVFFI9129JCPC/@@download/IGVFFI9129JCPC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/6c23236a-c03c-4b5c-9061-193d580df6d5/IGVFFI9129JCPC.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/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW288_S3_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2364WFHK/",
"accession": "IGVFFI2364WFHK",
"aliases": [
"gary-hon:LW288_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:55:41.361170+00:00",
"file_format": "fastq",
"file_size": 814782855,
"href": "/sequence-files/IGVFFI2364WFHK/@@download/IGVFFI2364WFHK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/ffd07308-b466-4e66-9ba5-24720b6d1a1c/IGVFFI2364WFHK.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/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW288_S3_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2717TTOD/",
"accession": "IGVFFI2717TTOD",
"aliases": [
"gary-hon:LW288_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:57:34.062423+00:00",
"file_format": "fastq",
"file_size": 741754918,
"href": "/sequence-files/IGVFFI2717TTOD/@@download/IGVFFI2717TTOD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/4546eebc-663a-47f2-a3a5-b4b34998eb58/IGVFFI2717TTOD.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/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW288_S3_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5124UFYH/",
"accession": "IGVFFI5124UFYH",
"aliases": [
"gary-hon:LW288_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:58:09.263934+00:00",
"file_format": "fastq",
"file_size": 6397556756,
"href": "/sequence-files/IGVFFI5124UFYH/@@download/IGVFFI5124UFYH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/849a8be3-d1cc-49c9-816e-898de00ee871/IGVFFI5124UFYH.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/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW288_S3_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1526NFSS/",
"accession": "IGVFFI1526NFSS",
"aliases": [
"gary-hon:LW288_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:55:52.308194+00:00",
"file_format": "fastq",
"file_size": 2710882978,
"href": "/sequence-files/IGVFFI1526NFSS/@@download/IGVFFI1526NFSS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/8ebdede4-ffe7-4224-9383-07b777af2a3f/IGVFFI1526NFSS.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/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW288_S3_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9278DMWO/",
"accession": "IGVFFI9278DMWO",
"aliases": [
"gary-hon:LW288_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:56:19.493060+00:00",
"file_format": "fastq",
"file_size": 7025040211,
"href": "/sequence-files/IGVFFI9278DMWO/@@download/IGVFFI9278DMWO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/8cf19f2e-f654-4e3e-9877-9be4b72121c1/IGVFFI9278DMWO.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
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"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW288_S3_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5388NBDD/",
"accession": "IGVFFI5388NBDD",
"aliases": [
"gary-hon:LW288_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:57:23.218935+00:00",
"file_format": "fastq",
"file_size": 733979582,
"href": "/sequence-files/IGVFFI5388NBDD/@@download/IGVFFI5388NBDD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/acf004db-9e89-44ec-ad2f-5ede10e0ba9a/IGVFFI5388NBDD.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/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW288_S3_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3403UWCY/",
"accession": "IGVFFI3403UWCY",
"aliases": [
"gary-hon:LW288_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:57:44.178156+00:00",
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"href": "/sequence-files/IGVFFI3403UWCY/@@download/IGVFFI3403UWCY.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/2023/2023-11-03-McDermott-NextSeq.10X.run1/2023-11-03/outs/fastq_path/AAC7TGLHV//LW288_S3_L002_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7340YDHF/"
],
"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/IGVFSM9411HZLU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9411HZLU",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW288"
],
"classifications": [
"cell line"
],
"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) cell line (cellular sub pool: subpool_LW288), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-03-04T19:55:30.833750+00:00",
"submitter_comment": "Transcriptiome for LW288",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "06d6a5ac-054c-446f-b13e-073830775300"
}