{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1050IJPU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1050IJPU",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_PB_LW273"
],
"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 [IGVFDS7977FNRB](/auxiliary-sets/IGVFDS7977FNRB/) has sequence file(s) [IGVFFI2670IEKQ](/sequence-files/IGVFFI2670IEKQ/), [IGVFFI1578SEWC](/sequence-files/IGVFFI1578SEWC/), [IGVFFI4135OJKZ](/sequence-files/IGVFFI4135OJKZ/), [IGVFFI2260FAWA](/sequence-files/IGVFFI2260FAWA/) 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/IGVFDS7977FNRB/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7977FNRB](/auxiliary-sets/IGVFDS7977FNRB/) has sequence file(s): [IGVFFI2670IEKQ](/sequence-files/IGVFFI2670IEKQ/), [IGVFFI1578SEWC](/sequence-files/IGVFFI1578SEWC/), [IGVFFI4135OJKZ](/sequence-files/IGVFFI4135OJKZ/), [IGVFFI2260FAWA](/sequence-files/IGVFFI2260FAWA/) 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/IGVFDS7977FNRB/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1050IJPU](/measurement-sets/IGVFDS1050IJPU/) has sequence file(s) [IGVFFI3288JJYA](/sequence-files/IGVFFI3288JJYA/), [IGVFFI4561QAWI](/sequence-files/IGVFFI4561QAWI/), [IGVFFI5586LATM](/sequence-files/IGVFFI5586LATM/), [IGVFFI2923CVQG](/sequence-files/IGVFFI2923CVQG/) 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/IGVFDS1050IJPU/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1050IJPU](/measurement-sets/IGVFDS1050IJPU/) has sequence file(s): [IGVFFI3288JJYA](/sequence-files/IGVFFI3288JJYA/), [IGVFFI4561QAWI](/sequence-files/IGVFFI4561QAWI/), [IGVFFI5586LATM](/sequence-files/IGVFFI5586LATM/), [IGVFFI2923CVQG](/sequence-files/IGVFFI2923CVQG/) 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/IGVFDS1050IJPU/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5841QQSW](/auxiliary-sets/IGVFDS5841QQSW/) has sequence file(s) [IGVFFI0200HHMT](/sequence-files/IGVFFI0200HHMT/), [IGVFFI2329KMIP](/sequence-files/IGVFFI2329KMIP/), [IGVFFI6130CCFL](/sequence-files/IGVFFI6130CCFL/), [IGVFFI2017KAHP](/sequence-files/IGVFFI2017KAHP/) 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/IGVFDS5841QQSW/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5841QQSW](/auxiliary-sets/IGVFDS5841QQSW/) has sequence file(s): [IGVFFI0200HHMT](/sequence-files/IGVFFI0200HHMT/), [IGVFFI2329KMIP](/sequence-files/IGVFFI2329KMIP/), [IGVFFI6130CCFL](/sequence-files/IGVFFI6130CCFL/), [IGVFFI2017KAHP](/sequence-files/IGVFFI2017KAHP/) 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/IGVFDS5841QQSW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5841QQSW/",
"accession": "IGVFDS5841QQSW",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_PB_LW273"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7977FNRB/",
"accession": "IGVFDS7977FNRB",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_HTO_PB_LW273"
],
"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": "2024-04-25T21:58:45.813274+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/IGVFFI3288JJYA/",
"accession": "IGVFFI3288JJYA",
"aliases": [
"gary-hon:LW273_8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:37:28.998951+00:00",
"file_format": "fastq",
"file_size": 11936114651,
"href": "/sequence-files/IGVFFI3288JJYA/@@download/IGVFFI3288JJYA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/3d6a43fb-323c-4db7-bcd4-a7662607d743/IGVFFI3288JJYA.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//LW273_S5_L008_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4561QAWI/",
"accession": "IGVFFI4561QAWI",
"aliases": [
"gary-hon:LW273_8_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:35:16.491931+00:00",
"file_format": "fastq",
"file_size": 1014752391,
"href": "/sequence-files/IGVFFI4561QAWI/@@download/IGVFFI4561QAWI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/64f63963-b6eb-4b17-a72d-5ad4860b6e69/IGVFFI4561QAWI.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//LW273_S5_L008_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5586LATM/",
"accession": "IGVFFI5586LATM",
"aliases": [
"gary-hon:LW273_8_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:35:29.364312+00:00",
"file_format": "fastq",
"file_size": 1083071364,
"href": "/sequence-files/IGVFFI5586LATM/@@download/IGVFFI5586LATM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/0d35cd68-64ef-45da-9950-9be22c9331f7/IGVFFI5586LATM.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//LW273_S5_L008_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2923CVQG/",
"accession": "IGVFFI2923CVQG",
"aliases": [
"gary-hon:LW273_8_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:35:42.373614+00:00",
"file_format": "fastq",
"file_size": 11909499932,
"href": "/sequence-files/IGVFFI2923CVQG/@@download/IGVFFI2923CVQG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/48ff1d3c-65ea-40f4-abe1-0140debc6cdd/IGVFFI2923CVQG.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//LW273_S5_L008_R1_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/IGVFSM1063UQVF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1063UQVF",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_PB_LW273"
],
"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_LW273), 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": "2024-04-25T22:35:16.491931+00:00",
"submitter_comment": "Transcriptiome for LW273",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "d65018f9-7426-48b4-9ad6-586eba425ea1"
}