{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3625MSZP/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3625MSZP",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_HTO_LW268"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS3625MSZP](/auxiliary-sets/IGVFDS3625MSZP/) has sequence file(s) [IGVFFI3144NXDU](/sequence-files/IGVFFI3144NXDU/), [IGVFFI5357FGJY](/sequence-files/IGVFFI5357FGJY/), [IGVFFI4477BFFF](/sequence-files/IGVFFI4477BFFF/), [IGVFFI7018AWNR](/sequence-files/IGVFFI7018AWNR/) 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/IGVFDS3625MSZP/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3625MSZP](/auxiliary-sets/IGVFDS3625MSZP/) has sequence file(s): [IGVFFI3144NXDU](/sequence-files/IGVFFI3144NXDU/), [IGVFFI5357FGJY](/sequence-files/IGVFFI5357FGJY/), [IGVFFI4477BFFF](/sequence-files/IGVFFI4477BFFF/), [IGVFFI7018AWNR](/sequence-files/IGVFFI7018AWNR/) 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/IGVFDS3625MSZP/"
}
]
},
"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": "2024-02-15T23:36:04.719560+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "cell hashing barcode sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI3144NXDU/",
"accession": "IGVFFI3144NXDU",
"aliases": [
"gary-hon:LW268C_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:42:04.988612+00:00",
"file_format": "fastq",
"file_size": 113006315,
"href": "/sequence-files/IGVFFI3144NXDU/@@download/IGVFFI3144NXDU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/cbd390f7-dbd1-4dca-a098-29fa33c5bf86/IGVFFI3144NXDU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-07-McDermott-NextSeq.10X.run1.sgRNA_HTO/2023-07-07/outs/fastq_path/AACV7CFM5/LW268C_S16_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5357FGJY/",
"accession": "IGVFFI5357FGJY",
"aliases": [
"gary-hon:LW268C_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:42:19.940428+00:00",
"file_format": "fastq",
"file_size": 284819947,
"href": "/sequence-files/IGVFFI5357FGJY/@@download/IGVFFI5357FGJY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/df5811fc-956c-425c-92e8-03070468116f/IGVFFI5357FGJY.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-07-McDermott-NextSeq.10X.run1.sgRNA_HTO/2023-07-07/outs/fastq_path/AACV7CFM5/LW268C_S16_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4477BFFF/",
"accession": "IGVFFI4477BFFF",
"aliases": [
"gary-hon:LW268C_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:42:30.384104+00:00",
"file_format": "fastq",
"file_size": 720619513,
"href": "/sequence-files/IGVFFI4477BFFF/@@download/IGVFFI4477BFFF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/c7b536e1-35fb-4132-a151-06970c872fe1/IGVFFI4477BFFF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-07-McDermott-NextSeq.10X.run1.sgRNA_HTO/2023-07-07/outs/fastq_path/AACV7CFM5/LW268C_S16_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7018AWNR/",
"accession": "IGVFFI7018AWNR",
"aliases": [
"gary-hon:LW268C_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-20T20:42:09.965155+00:00",
"file_format": "fastq",
"file_size": 107571838,
"href": "/sequence-files/IGVFFI7018AWNR/@@download/IGVFFI7018AWNR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/20/88ab8361-719f-4919-bc41-22f518860451/IGVFFI7018AWNR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-07-07-McDermott-NextSeq.10X.run1.sgRNA_HTO/2023-07-07/outs/fastq_path/AACV7CFM5/LW268C_S16_L001_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4003HZAB/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS5173WYKU/",
"accession": "IGVFDS5173WYKU",
"aliases": [
"gary-hon:CM_Pilot_2_Lenti_RNA_LW268"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"notes": "File_set_type enum cell hashing has been renamed to be cell hashing barcode sequencing.",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2215YBLM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2215YBLM",
"aliases": [
"nikhil-munshi:differentited_WTC11_CM_Pilot1_Lenti_LW268"
],
"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_LW268), 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": "12",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-02-20T20:42:04.988612+00:00",
"summary": "cell hashing barcode sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "b6f2cace-88a9-441e-9010-d4a871a1fec7"
}