{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS9976WMCI/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS9976WMCI",
"aliases": [
"gary-hon:CM_Pilot_2_PB_sgRNA_LW236"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9976WMCI](/auxiliary-sets/IGVFDS9976WMCI/) has sequence file(s) [IGVFFI3939YRKP](/sequence-files/IGVFFI3939YRKP/), [IGVFFI8413FBXY](/sequence-files/IGVFFI8413FBXY/), [IGVFFI7863LXLL](/sequence-files/IGVFFI7863LXLL/), [IGVFFI1976BTXC](/sequence-files/IGVFFI1976BTXC/), [IGVFFI8279OHEK](/sequence-files/IGVFFI8279OHEK/), [IGVFFI1480DNXC](/sequence-files/IGVFFI1480DNXC/), [IGVFFI8928YFKN](/sequence-files/IGVFFI8928YFKN/), [IGVFFI8077IAPC](/sequence-files/IGVFFI8077IAPC/) 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/IGVFDS9976WMCI/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9976WMCI](/auxiliary-sets/IGVFDS9976WMCI/) has sequence file(s): [IGVFFI3939YRKP](/sequence-files/IGVFFI3939YRKP/), [IGVFFI8413FBXY](/sequence-files/IGVFFI8413FBXY/), [IGVFFI7863LXLL](/sequence-files/IGVFFI7863LXLL/), [IGVFFI1976BTXC](/sequence-files/IGVFFI1976BTXC/), [IGVFFI8279OHEK](/sequence-files/IGVFFI8279OHEK/), [IGVFFI1480DNXC](/sequence-files/IGVFFI1480DNXC/), [IGVFFI8928YFKN](/sequence-files/IGVFFI8928YFKN/), [IGVFFI8077IAPC](/sequence-files/IGVFFI8077IAPC/) 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/IGVFDS9976WMCI/"
}
]
},
"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": "2024-02-15T23:35:43.830643+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI3939YRKP/",
"accession": "IGVFFI3939YRKP",
"aliases": [
"gary-hon:LW236B-2_2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:30:08.703853+00:00",
"file_format": "fastq",
"file_size": 133887436,
"href": "/sequence-files/IGVFFI3939YRKP/@@download/IGVFFI3939YRKP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/0278854a-702d-4b81-abb8-a92dc2b7d77e/IGVFFI3939YRKP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW236B-2_S6_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8413FBXY/",
"accession": "IGVFFI8413FBXY",
"aliases": [
"gary-hon:LW236B-2_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:30:03.122668+00:00",
"file_format": "fastq",
"file_size": 157524766,
"href": "/sequence-files/IGVFFI8413FBXY/@@download/IGVFFI8413FBXY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/64d8ae84-d460-47d5-9a52-b15f2707d220/IGVFFI8413FBXY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW236B-2_S6_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7863LXLL/",
"accession": "IGVFFI7863LXLL",
"aliases": [
"gary-hon:LW236B-2_2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:30:13.820645+00:00",
"file_format": "fastq",
"file_size": 479305852,
"href": "/sequence-files/IGVFFI7863LXLL/@@download/IGVFFI7863LXLL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/3018b755-749f-47bb-ae2c-673a02d12887/IGVFFI7863LXLL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW236B-2_S6_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1976BTXC/",
"accession": "IGVFFI1976BTXC",
"aliases": [
"gary-hon:LW236B-2_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:29:34.337512+00:00",
"file_format": "fastq",
"file_size": 164371729,
"href": "/sequence-files/IGVFFI1976BTXC/@@download/IGVFFI1976BTXC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/07f32007-1674-43b2-b585-785dc9f5c429/IGVFFI1976BTXC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW236B-2_S6_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8279OHEK/",
"accession": "IGVFFI8279OHEK",
"aliases": [
"gary-hon:LW236B-2_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:29:40.059720+00:00",
"file_format": "fastq",
"file_size": 143668490,
"href": "/sequence-files/IGVFFI8279OHEK/@@download/IGVFFI8279OHEK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/01bf9df0-bd1b-4fd1-aa7f-91d0947686c8/IGVFFI8279OHEK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW236B-2_S6_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1480DNXC/",
"accession": "IGVFFI1480DNXC",
"aliases": [
"gary-hon:LW236B-2_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:29:45.309061+00:00",
"file_format": "fastq",
"file_size": 493092167,
"href": "/sequence-files/IGVFFI1480DNXC/@@download/IGVFFI1480DNXC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/a639d41f-e997-4d70-ae22-772aef325f94/IGVFFI1480DNXC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW236B-2_S6_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8928YFKN/",
"accession": "IGVFFI8928YFKN",
"aliases": [
"gary-hon:LW236B-2_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:29:53.548377+00:00",
"file_format": "fastq",
"file_size": 647792604,
"href": "/sequence-files/IGVFFI8928YFKN/@@download/IGVFFI8928YFKN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/07b6df7f-53ec-4bc0-a1b6-bd643390d30e/IGVFFI8928YFKN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW236B-2_S6_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8077IAPC/",
"accession": "IGVFFI8077IAPC",
"aliases": [
"gary-hon:LW236B-2_2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-21T18:30:22.131378+00:00",
"file_format": "fastq",
"file_size": 624999197,
"href": "/sequence-files/IGVFFI8077IAPC/@@download/IGVFFI8077IAPC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/21/62d1cf6f-034d-454c-82c4-a28b188a3933/IGVFFI8077IAPC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-03-24-McDermott-NextSeq.10X/2023-03-24/outs/fastq_path/AAC235NHV/LW236B-2_S6_L002_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9192YMGI/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0890CUXC/",
"accession": "IGVFDS0890CUXC",
"aliases": [
"gary-hon:CM_Pilot_2_PB_RNA_LW236"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5652SBGF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5652SBGF",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_PB_LW236"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS9629YZLO/"
],
"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_LW266), male, Homo sapiens modified with CRISPRi Sp-dCas9, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-02-21T18:29:34.337512+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "8d690f7d-8b80-4e06-a069-c9f5d4debfd6"
}