{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2083PYXJ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2083PYXJ",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_PB_LW275"
],
"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 [IGVFDS4359ZBDC](/auxiliary-sets/IGVFDS4359ZBDC/) has sequence file(s) [IGVFFI0803YNRO](/sequence-files/IGVFFI0803YNRO/), [IGVFFI8989OYHB](/sequence-files/IGVFFI8989OYHB/), [IGVFFI9089SVDS](/sequence-files/IGVFFI9089SVDS/), [IGVFFI4964UHUV](/sequence-files/IGVFFI4964UHUV/) 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/IGVFDS4359ZBDC/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4359ZBDC](/auxiliary-sets/IGVFDS4359ZBDC/) has sequence file(s): [IGVFFI0803YNRO](/sequence-files/IGVFFI0803YNRO/), [IGVFFI8989OYHB](/sequence-files/IGVFFI8989OYHB/), [IGVFFI9089SVDS](/sequence-files/IGVFFI9089SVDS/), [IGVFFI4964UHUV](/sequence-files/IGVFFI4964UHUV/) 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/IGVFDS4359ZBDC/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2083PYXJ](/measurement-sets/IGVFDS2083PYXJ/) has sequence file(s) [IGVFFI2973HESL](/sequence-files/IGVFFI2973HESL/), [IGVFFI1482IPHD](/sequence-files/IGVFFI1482IPHD/), [IGVFFI6057IAGQ](/sequence-files/IGVFFI6057IAGQ/), [IGVFFI1894TYJR](/sequence-files/IGVFFI1894TYJR/) 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/IGVFDS2083PYXJ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2083PYXJ](/measurement-sets/IGVFDS2083PYXJ/) has sequence file(s): [IGVFFI2973HESL](/sequence-files/IGVFFI2973HESL/), [IGVFFI1482IPHD](/sequence-files/IGVFFI1482IPHD/), [IGVFFI6057IAGQ](/sequence-files/IGVFFI6057IAGQ/), [IGVFFI1894TYJR](/sequence-files/IGVFFI1894TYJR/) 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/IGVFDS2083PYXJ/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9721PIUS](/auxiliary-sets/IGVFDS9721PIUS/) has sequence file(s) [IGVFFI1337DHGD](/sequence-files/IGVFFI1337DHGD/), [IGVFFI7370GQOW](/sequence-files/IGVFFI7370GQOW/), [IGVFFI7612JPXT](/sequence-files/IGVFFI7612JPXT/), [IGVFFI4081JSOK](/sequence-files/IGVFFI4081JSOK/) 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/IGVFDS9721PIUS/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9721PIUS](/auxiliary-sets/IGVFDS9721PIUS/) has sequence file(s): [IGVFFI1337DHGD](/sequence-files/IGVFFI1337DHGD/), [IGVFFI7370GQOW](/sequence-files/IGVFFI7370GQOW/), [IGVFFI7612JPXT](/sequence-files/IGVFFI7612JPXT/), [IGVFFI4081JSOK](/sequence-files/IGVFFI4081JSOK/) 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/IGVFDS9721PIUS/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9721PIUS/",
"accession": "IGVFDS9721PIUS",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_PB_LW275"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS4359ZBDC/",
"accession": "IGVFDS4359ZBDC",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_HTO_PB_LW275"
],
"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": "2024-04-25T21:58:48.168176+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2718IDDQ/",
"accession": "IGVFDO2718IDDQ",
"aliases": [
"igvf:donor_of_H9"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI2973HESL/",
"accession": "IGVFFI2973HESL",
"aliases": [
"gary-hon:LW275_8_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:43:09.350791+00:00",
"file_format": "fastq",
"file_size": 1010107130,
"href": "/sequence-files/IGVFFI2973HESL/@@download/IGVFFI2973HESL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/ea534191-f81d-4a09-9a87-e10270a3209d/IGVFFI2973HESL.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/2023/2023-10-25-McDermott-NovaSeq.lane8.10X/10X//LW275_S7_L008_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1482IPHD/",
"accession": "IGVFFI1482IPHD",
"aliases": [
"gary-hon:LW275_8_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:43:39.526304+00:00",
"file_format": "fastq",
"file_size": 12945114914,
"href": "/sequence-files/IGVFFI1482IPHD/@@download/IGVFFI1482IPHD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/c6b1b06a-d597-4942-81f1-662eae200c8c/IGVFFI1482IPHD.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/2023/2023-10-25-McDermott-NovaSeq.lane8.10X/10X//LW275_S7_L008_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6057IAGQ/",
"accession": "IGVFFI6057IAGQ",
"aliases": [
"gary-hon:LW275_8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:45:33.559162+00:00",
"file_format": "fastq",
"file_size": 12992037093,
"href": "/sequence-files/IGVFFI6057IAGQ/@@download/IGVFFI6057IAGQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/59a7efd1-7730-4a11-8859-d8ae258923ad/IGVFFI6057IAGQ.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/2023/2023-10-25-McDermott-NovaSeq.lane8.10X/10X//LW275_S7_L008_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1894TYJR/",
"accession": "IGVFFI1894TYJR",
"aliases": [
"gary-hon:LW275_8_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:43:23.098743+00:00",
"file_format": "fastq",
"file_size": 1109844639,
"href": "/sequence-files/IGVFFI1894TYJR/@@download/IGVFFI1894TYJR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/96769d2c-b209-4367-aa3a-8ed6cccab67d/IGVFFI1894TYJR.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/2023/2023-10-25-McDermott-NovaSeq.lane8.10X/10X//LW275_S7_L008_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4762GRIW/"
],
"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/IGVFSM9532RAXS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9532RAXS",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_PB_LW275"
],
"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_0003045/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H9"
],
"status": "released",
"summary": "H9",
"term_name": "H9"
}
],
"status": "preview",
"summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW275), female, 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": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-04-25T22:43:09.350791+00:00",
"submitter_comment": "Transcriptiome for LW275",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "03a5a83d-cf60-41f9-af26-ab2c63a466fa"
}