{
"@context": "/terms/",
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"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS8386FNRJ",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane1_CS1"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8386FNRJ](/auxiliary-sets/IGVFDS8386FNRJ/) has sequence file(s): [IGVFFI3534JLPF](/sequence-files/IGVFFI3534JLPF/), [IGVFFI4980GVVC](/sequence-files/IGVFFI4980GVVC/), [IGVFFI9263MTNB](/sequence-files/IGVFFI9263MTNB/), [IGVFFI3537WAMV](/sequence-files/IGVFFI3537WAMV/), [IGVFFI6258TUAO](/sequence-files/IGVFFI6258TUAO/), [IGVFFI6689DLGE](/sequence-files/IGVFFI6689DLGE/), [IGVFFI0070OAUF](/sequence-files/IGVFFI0070OAUF/), [IGVFFI2908NAIM](/sequence-files/IGVFFI2908NAIM/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS8386FNRJ/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM7750SNNY](/in-vitro-systems/IGVFSM7750SNNY/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM7750SNNY/"
}
]
},
"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"
},
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{
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{
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"accession": "IGVFFI2463QNJD",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "GRCh38 guide RNA sequences"
}
],
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"summary": "guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2023-12-08T23:52:05.762124+00:00",
"donors": [
{
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"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
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],
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},
{
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],
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"creation_timestamp": "2023-12-09T00:50:57.034977+00:00",
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"s3_uri": "s3://igvf-files/2023/12/09/a0eaee33-5e89-4ba3-b8ba-a3ca0867279b/IGVFFI4980GVVC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "released",
"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_1/CS1_1_S5_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
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],
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"creation_timestamp": "2023-12-09T00:51:00.492108+00:00",
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"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "released",
"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_1/CS1_1_S5_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3537WAMV/",
"accession": "IGVFFI3537WAMV",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane1_seqlane2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:50:59.208018+00:00",
"file_format": "fastq",
"file_size": 340369705,
"href": "/sequence-files/IGVFFI3537WAMV/@@download/IGVFFI3537WAMV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/3aeb5043-316b-4fff-a61a-5df49e97ed1c/IGVFFI3537WAMV.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "released",
"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_1/CS1_1_S5_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
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"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane1_seqlane1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:50:54.735024+00:00",
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"file_size": 356417915,
"href": "/sequence-files/IGVFFI6258TUAO/@@download/IGVFFI6258TUAO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/3fdb7bfb-fc6a-4a77-a783-03ef7982cb7a/IGVFFI6258TUAO.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "released",
"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_1/CS1_1_S5_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6689DLGE/",
"accession": "IGVFFI6689DLGE",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane1_seqlane1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:50:55.949835+00:00",
"file_format": "fastq",
"file_size": 1044468908,
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"s3_uri": "s3://igvf-files/2023/12/09/260c6f0b-67f9-4cb8-96f6-807582406b69/IGVFFI6689DLGE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "released",
"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_1/CS1_1_S5_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0070OAUF/",
"accession": "IGVFFI0070OAUF",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane1_seqlane2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:50:58.127910+00:00",
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"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_1/CS1_1_S5_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2908NAIM/",
"accession": "IGVFFI2908NAIM",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_CS1_10Xlane1_seqlane2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:51:01.550881+00:00",
"file_format": "fastq",
"file_size": 1089164603,
"href": "/sequence-files/IGVFFI2908NAIM/@@download/IGVFFI2908NAIM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/ff8f27d2-547e-4bcf-922b-3174afb4815e/IGVFFI2908NAIM.fastq.gz",
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"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_1/CS1_1_S5_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/IGVFDS9384BVGM/",
"accession": "IGVFDS9384BVGM",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane1_exprs"
],
"preferred_assay_title": "scCRISPR screen",
"status": "released"
}
],
"publications": [
{
"@id": "/publications/20fcbdbb-5a47-41c6-b80b-e6dd0e8a8d3e/",
"publication_identifiers": [
"doi:10.1038/s41467-024-52490-4"
],
"status": "released"
}
],
"release_timestamp": "2024-08-13T20:47:21.563052+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7750SNNY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7750SNNY",
"aliases": [
"jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane1"
],
"cellular_sub_pool": "10Xlane1",
"classifications": [
"differentiated cell specimen"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/",
"modality": "activation",
"status": "released"
}
],
"sample_terms": [
{
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"@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: 10Xlane1), male, Homo sapiens modified with CRISPRa Sp-dCas9-VPH, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000540/",
"status": "released",
"term_name": "neuron"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"submitted_files_timestamp": "2023-12-09T00:50:53.650937+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": "ba54d793-6bd3-4793-b689-f1798ad3d759"
}