{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5429CXNB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5429CXNB",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_LW286"
],
"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 [IGVFDS3465KEWH](/auxiliary-sets/IGVFDS3465KEWH/) has sequence file(s) [IGVFFI3046CEDS](/sequence-files/IGVFFI3046CEDS/), [IGVFFI2095GWCE](/sequence-files/IGVFFI2095GWCE/), [IGVFFI4014VOTR](/sequence-files/IGVFFI4014VOTR/), [IGVFFI6603ZNLC](/sequence-files/IGVFFI6603ZNLC/) 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/IGVFDS3465KEWH/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3465KEWH](/auxiliary-sets/IGVFDS3465KEWH/) has sequence file(s): [IGVFFI3046CEDS](/sequence-files/IGVFFI3046CEDS/), [IGVFFI2095GWCE](/sequence-files/IGVFFI2095GWCE/), [IGVFFI4014VOTR](/sequence-files/IGVFFI4014VOTR/), [IGVFFI6603ZNLC](/sequence-files/IGVFFI6603ZNLC/) 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/IGVFDS3465KEWH/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1128FXRR](/auxiliary-sets/IGVFDS1128FXRR/) has sequence file(s) [IGVFFI9511EKXQ](/sequence-files/IGVFFI9511EKXQ/), [IGVFFI6053YIFW](/sequence-files/IGVFFI6053YIFW/), [IGVFFI6212DKTA](/sequence-files/IGVFFI6212DKTA/), [IGVFFI6700ENLR](/sequence-files/IGVFFI6700ENLR/) 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/IGVFDS1128FXRR/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1128FXRR](/auxiliary-sets/IGVFDS1128FXRR/) has sequence file(s): [IGVFFI9511EKXQ](/sequence-files/IGVFFI9511EKXQ/), [IGVFFI6053YIFW](/sequence-files/IGVFFI6053YIFW/), [IGVFFI6212DKTA](/sequence-files/IGVFFI6212DKTA/), [IGVFFI6700ENLR](/sequence-files/IGVFFI6700ENLR/) 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/IGVFDS1128FXRR/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5429CXNB](/measurement-sets/IGVFDS5429CXNB/) has sequence file(s) [IGVFFI2177DFRH](/sequence-files/IGVFFI2177DFRH/), [IGVFFI3868KDUU](/sequence-files/IGVFFI3868KDUU/), [IGVFFI8142CIDW](/sequence-files/IGVFFI8142CIDW/), [IGVFFI5020EGXD](/sequence-files/IGVFFI5020EGXD/), [IGVFFI0160DJHO](/sequence-files/IGVFFI0160DJHO/), [IGVFFI8734WGHA](/sequence-files/IGVFFI8734WGHA/), [IGVFFI0871LPRK](/sequence-files/IGVFFI0871LPRK/), [IGVFFI7095FECZ](/sequence-files/IGVFFI7095FECZ/) 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/IGVFDS5429CXNB/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5429CXNB](/measurement-sets/IGVFDS5429CXNB/) has sequence file(s): [IGVFFI2177DFRH](/sequence-files/IGVFFI2177DFRH/), [IGVFFI3868KDUU](/sequence-files/IGVFFI3868KDUU/), [IGVFFI8142CIDW](/sequence-files/IGVFFI8142CIDW/), [IGVFFI5020EGXD](/sequence-files/IGVFFI5020EGXD/), [IGVFFI0160DJHO](/sequence-files/IGVFFI0160DJHO/), [IGVFFI8734WGHA](/sequence-files/IGVFFI8734WGHA/), [IGVFFI0871LPRK](/sequence-files/IGVFFI0871LPRK/), [IGVFFI7095FECZ](/sequence-files/IGVFFI7095FECZ/) 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/IGVFDS5429CXNB/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1128FXRR/",
"accession": "IGVFDS1128FXRR",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_sgRNA_LW286"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS3465KEWH/",
"accession": "IGVFDS3465KEWH",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_iPSC_HTO_LW286"
],
"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": "2024-02-21T21:28:50.109383+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/IGVFFI2177DFRH/",
"accession": "IGVFFI2177DFRH",
"aliases": [
"gary-hon:LW286_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:48:05.129836+00:00",
"file_format": "fastq",
"file_size": 834377613,
"href": "/sequence-files/IGVFFI2177DFRH/@@download/IGVFFI2177DFRH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/3cb44fcd-6dba-46f6-a4cd-2a625686c245/IGVFFI2177DFRH.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//LW286_S1_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3868KDUU/",
"accession": "IGVFFI3868KDUU",
"aliases": [
"gary-hon:LW286_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:48:17.114209+00:00",
"file_format": "fastq",
"file_size": 859314429,
"href": "/sequence-files/IGVFFI3868KDUU/@@download/IGVFFI3868KDUU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/6197f247-7038-4b12-81ee-1fb8bdcdef91/IGVFFI3868KDUU.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//LW286_S1_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8142CIDW/",
"accession": "IGVFFI8142CIDW",
"aliases": [
"gary-hon:LW286_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:48:28.505387+00:00",
"file_format": "fastq",
"file_size": 2516835246,
"href": "/sequence-files/IGVFFI8142CIDW/@@download/IGVFFI8142CIDW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/eaecc74a-8c7d-433e-8cec-b1218a34925c/IGVFFI8142CIDW.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//LW286_S1_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5020EGXD/",
"accession": "IGVFFI5020EGXD",
"aliases": [
"gary-hon:LW286_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:48:53.851358+00:00",
"file_format": "fastq",
"file_size": 6487953282,
"href": "/sequence-files/IGVFFI5020EGXD/@@download/IGVFFI5020EGXD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/99cd06b6-96b0-4fe8-9a06-ab3e65e69758/IGVFFI5020EGXD.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//LW286_S1_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0160DJHO/",
"accession": "IGVFFI0160DJHO",
"aliases": [
"gary-hon:LW286_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:49:53.128618+00:00",
"file_format": "fastq",
"file_size": 787212709,
"href": "/sequence-files/IGVFFI0160DJHO/@@download/IGVFFI0160DJHO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/1c51c628-3fe7-405f-8b3e-aeabee933744/IGVFFI0160DJHO.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//LW286_S1_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8734WGHA/",
"accession": "IGVFFI8734WGHA",
"aliases": [
"gary-hon:LW286_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:50:03.826342+00:00",
"file_format": "fastq",
"file_size": 815766459,
"href": "/sequence-files/IGVFFI8734WGHA/@@download/IGVFFI8734WGHA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/eab275bd-b971-4155-a8f2-73fc9023ca25/IGVFFI8734WGHA.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//LW286_S1_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0871LPRK/",
"accession": "IGVFFI0871LPRK",
"aliases": [
"gary-hon:LW286_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:50:14.966303+00:00",
"file_format": "fastq",
"file_size": 2390988265,
"href": "/sequence-files/IGVFFI0871LPRK/@@download/IGVFFI0871LPRK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/7318b1cf-13f8-4354-a9fc-550a5b860be3/IGVFFI0871LPRK.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//LW286_S1_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7095FECZ/",
"accession": "IGVFFI7095FECZ",
"aliases": [
"gary-hon:LW286_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-04T19:50:39.001783+00:00",
"file_format": "fastq",
"file_size": 6152600298,
"href": "/sequence-files/IGVFFI7095FECZ/@@download/IGVFFI7095FECZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/04/3b362ca2-3da3-41f4-904c-62357f449a07/IGVFFI7095FECZ.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//LW286_S1_L002_R2_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/IGVFSM2726ORRN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2726ORRN",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW286"
],
"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_LW286), 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": "2024-03-04T19:48:05.129836+00:00",
"submitter_comment": "Transcriptiome for LW286",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "acb59998-eb3d-4a8e-9afa-9a8a110c1a9d"
}