{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS7598WPXV/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS7598WPXV",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane4_CS1"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7598WPXV](/auxiliary-sets/IGVFDS7598WPXV/) has sequence file(s): [IGVFFI7501QBYI](/sequence-files/IGVFFI7501QBYI/), [IGVFFI3432JHMF](/sequence-files/IGVFFI3432JHMF/), [IGVFFI8644VEVN](/sequence-files/IGVFFI8644VEVN/), [IGVFFI1501KPWU](/sequence-files/IGVFFI1501KPWU/), [IGVFFI7243XYXN](/sequence-files/IGVFFI7243XYXN/), [IGVFFI5101PVJN](/sequence-files/IGVFFI5101PVJN/), [IGVFFI5318WDGT](/sequence-files/IGVFFI5318WDGT/), [IGVFFI2675LZFM](/sequence-files/IGVFFI2675LZFM/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS7598WPXV/"
}
]
},
"award": {
"@id": "/awards/HG011966/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/eb543cda-67b7-493c-84eb-187d0dac13ba/",
"title": "Jay Shendure"
},
"title": "Massively parallel characterization of variants and elements impacting transcriptional regulation in dynamic cellular systems"
},
"control_for": [],
"creation_timestamp": "2023-12-08T23:52:08.103425+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/IGVFFI7501QBYI/",
"accession": "IGVFFI7501QBYI",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane4_seqlane1_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:24.133981+00:00",
"file_format": "fastq",
"file_size": 1151144445,
"href": "/sequence-files/IGVFFI7501QBYI/@@download/IGVFFI7501QBYI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/78e135ce-d044-40c8-86e1-1f54e0d351a9/IGVFFI7501QBYI.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_4/CS1_4_S8_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3432JHMF/",
"accession": "IGVFFI3432JHMF",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane4_seqlane1_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:25.206725+00:00",
"file_format": "fastq",
"file_size": 1463334174,
"href": "/sequence-files/IGVFFI3432JHMF/@@download/IGVFFI3432JHMF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/276370d4-fa0b-48b8-b466-1b9aac4eec6b/IGVFFI3432JHMF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_4/CS1_4_S8_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8644VEVN/",
"accession": "IGVFFI8644VEVN",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane4_seqlane2_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:29.732380+00:00",
"file_format": "fastq",
"file_size": 1062130033,
"href": "/sequence-files/IGVFFI8644VEVN/@@download/IGVFFI8644VEVN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/6069c667-bfb8-46a4-a36e-9fded4d1ed26/IGVFFI8644VEVN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_4/CS1_4_S8_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1501KPWU/",
"accession": "IGVFFI1501KPWU",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane4_seqlane1_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:21.993678+00:00",
"file_format": "fastq",
"file_size": 422427076,
"href": "/sequence-files/IGVFFI1501KPWU/@@download/IGVFFI1501KPWU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/917c2522-cbf6-4d19-a9d2-65ce34962ab5/IGVFFI1501KPWU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_4/CS1_4_S8_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7243XYXN/",
"accession": "IGVFFI7243XYXN",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane4_seqlane1_I2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:23.041493+00:00",
"file_format": "fastq",
"file_size": 393737299,
"href": "/sequence-files/IGVFFI7243XYXN/@@download/IGVFFI7243XYXN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/2bf56946-c960-4744-a33f-59a9f7497116/IGVFFI7243XYXN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_4/CS1_4_S8_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5101PVJN/",
"accession": "IGVFFI5101PVJN",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane4_seqlane2_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:27.168265+00:00",
"file_format": "fastq",
"file_size": 411037954,
"href": "/sequence-files/IGVFFI5101PVJN/@@download/IGVFFI5101PVJN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/36477a64-2534-416f-98ef-cd57541fcfdd/IGVFFI5101PVJN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_4/CS1_4_S8_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5318WDGT/",
"accession": "IGVFFI5318WDGT",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane4_seqlane2_I2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:28.648701+00:00",
"file_format": "fastq",
"file_size": 366303635,
"href": "/sequence-files/IGVFFI5318WDGT/@@download/IGVFFI5318WDGT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/dabe3de5-a1e7-4adb-9d24-ebe0d0f994ec/IGVFFI5318WDGT.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_4/CS1_4_S8_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2675LZFM/",
"accession": "IGVFFI2675LZFM",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane4_seqlane2_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:30.793086+00:00",
"file_format": "fastq",
"file_size": 1343874550,
"href": "/sequence-files/IGVFFI2675LZFM/@@download/IGVFFI2675LZFM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/7f0924af-c097-4714-8853-c9d7af4daf25/IGVFFI2675LZFM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/CS1_4/CS1_4_S8_L002_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4021XJLW/"
],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS2133JAFB/",
"accession": "IGVFDS2133JAFB",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane4_exprs"
],
"preferred_assay_title": "scCRISPR screen"
}
],
"publications": [
{
"@id": "/publications/20fcbdbb-5a47-41c6-b80b-e6dd0e8a8d3e/",
"publication_identifiers": [
"doi:10.1101/2023.03.28.534017"
]
}
],
"release_timestamp": "2024-08-13T20:47:23.261660+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8382KOXO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8382KOXO",
"aliases": [
"jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane4"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7581DNXF/"
],
"modifications": [
{
"@id": "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/",
"modality": "activation"
}
],
"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": "released",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to neuron for 19 days (cellular sub pool: 10Xlane4), male, Homo sapiens modified with CRISPRa Sp-dCas9-VPH, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000540/",
"term_name": "neuron"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"submitted_files_timestamp": "2023-12-09T00:51:21.993678+00:00",
"summary": "gRNA sequencing for scCRISPR activation screen integrating a guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci",
"uuid": "822751be-5815-44d0-bc39-7982015a1260"
}