{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0307GWPA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0307GWPA",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_PB_LW276"
],
"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 [IGVFDS4510VNEU](/auxiliary-sets/IGVFDS4510VNEU/) has sequence file(s) [IGVFFI4591SIBG](/sequence-files/IGVFFI4591SIBG/), [IGVFFI9879ZPBO](/sequence-files/IGVFFI9879ZPBO/), [IGVFFI2118VBKO](/sequence-files/IGVFFI2118VBKO/), [IGVFFI3883TQKS](/sequence-files/IGVFFI3883TQKS/) 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/IGVFDS4510VNEU/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4510VNEU](/auxiliary-sets/IGVFDS4510VNEU/) has sequence file(s): [IGVFFI4591SIBG](/sequence-files/IGVFFI4591SIBG/), [IGVFFI9879ZPBO](/sequence-files/IGVFFI9879ZPBO/), [IGVFFI2118VBKO](/sequence-files/IGVFFI2118VBKO/), [IGVFFI3883TQKS](/sequence-files/IGVFFI3883TQKS/) 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/IGVFDS4510VNEU/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS6756DREO](/auxiliary-sets/IGVFDS6756DREO/) has sequence file(s) [IGVFFI8741HEHC](/sequence-files/IGVFFI8741HEHC/), [IGVFFI2913YZIW](/sequence-files/IGVFFI2913YZIW/), [IGVFFI5373GJRK](/sequence-files/IGVFFI5373GJRK/), [IGVFFI6997KRUX](/sequence-files/IGVFFI6997KRUX/) 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/IGVFDS6756DREO/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6756DREO](/auxiliary-sets/IGVFDS6756DREO/) has sequence file(s): [IGVFFI8741HEHC](/sequence-files/IGVFFI8741HEHC/), [IGVFFI2913YZIW](/sequence-files/IGVFFI2913YZIW/), [IGVFFI5373GJRK](/sequence-files/IGVFFI5373GJRK/), [IGVFFI6997KRUX](/sequence-files/IGVFFI6997KRUX/) 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/IGVFDS6756DREO/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS0307GWPA](/measurement-sets/IGVFDS0307GWPA/) has sequence file(s) [IGVFFI9972QYOG](/sequence-files/IGVFFI9972QYOG/), [IGVFFI9642SDGR](/sequence-files/IGVFFI9642SDGR/), [IGVFFI2061HZUP](/sequence-files/IGVFFI2061HZUP/), [IGVFFI5777PTRZ](/sequence-files/IGVFFI5777PTRZ/) 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/IGVFDS0307GWPA/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0307GWPA](/measurement-sets/IGVFDS0307GWPA/) has sequence file(s): [IGVFFI9972QYOG](/sequence-files/IGVFFI9972QYOG/), [IGVFFI9642SDGR](/sequence-files/IGVFFI9642SDGR/), [IGVFFI2061HZUP](/sequence-files/IGVFFI2061HZUP/), [IGVFFI5777PTRZ](/sequence-files/IGVFFI5777PTRZ/) 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/IGVFDS0307GWPA/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4510VNEU/",
"accession": "IGVFDS4510VNEU",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_PB_LW276"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6756DREO/",
"accession": "IGVFDS6756DREO",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_HTO_PB_LW276"
],
"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": "2024-04-25T21:58:49.116703+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/IGVFFI9972QYOG/",
"accession": "IGVFFI9972QYOG",
"aliases": [
"gary-hon:LW276_8_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:47:51.174629+00:00",
"file_format": "fastq",
"file_size": 10383623517,
"href": "/sequence-files/IGVFFI9972QYOG/@@download/IGVFFI9972QYOG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/d02d7477-2f57-4255-82df-b62aa83d89a6/IGVFFI9972QYOG.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//LW276_S8_L008_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9642SDGR/",
"accession": "IGVFFI9642SDGR",
"aliases": [
"gary-hon:LW276_8_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:47:40.094136+00:00",
"file_format": "fastq",
"file_size": 851287584,
"href": "/sequence-files/IGVFFI9642SDGR/@@download/IGVFFI9642SDGR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/0925ee1f-2418-44c4-9522-4b7d2bf7b78c/IGVFFI9642SDGR.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//LW276_S8_L008_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2061HZUP/",
"accession": "IGVFFI2061HZUP",
"aliases": [
"gary-hon:LW276_8_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:49:23.250435+00:00",
"file_format": "fastq",
"file_size": 10384621792,
"href": "/sequence-files/IGVFFI2061HZUP/@@download/IGVFFI2061HZUP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/aa7fc2b3-c00f-4e54-949b-75f6957871ac/IGVFFI2061HZUP.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//LW276_S8_L008_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5777PTRZ/",
"accession": "IGVFFI5777PTRZ",
"aliases": [
"gary-hon:LW276_8_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-04-25T22:47:28.248245+00:00",
"file_format": "fastq",
"file_size": 904599937,
"href": "/sequence-files/IGVFFI5777PTRZ/@@download/IGVFFI5777PTRZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/04/25/62309be6-5a4c-4fbc-8cda-c647faf07ce4/IGVFFI5777PTRZ.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//LW276_S8_L008_I1_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/IGVFSM6716LOHW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6716LOHW",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_PB_LW276"
],
"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_LW276), 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": "2024-04-25T22:47:28.248245+00:00",
"submitter_comment": "Transcriptiome for LW276",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "0474d200-7886-47b2-b3e2-a191e86d684b"
}