{
"@context": "/terms/",
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"MeasurementSet",
"FileSet",
"Item"
],
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],
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"@id": "/assay-terms/OBI_0003660/",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"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 are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS8386FNRJ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9384BVGM](/measurement-sets/IGVFDS9384BVGM/) has sequence file(s): [IGVFFI8922YCWG](/sequence-files/IGVFFI8922YCWG/), [IGVFFI4869ZGAF](/sequence-files/IGVFFI4869ZGAF/), [IGVFFI7836XPXO](/sequence-files/IGVFFI7836XPXO/), [IGVFFI4547PKAZ](/sequence-files/IGVFFI4547PKAZ/), [IGVFFI9410BUAR](/sequence-files/IGVFFI9410BUAR/), [IGVFFI1249MWVF](/sequence-files/IGVFFI1249MWVF/), [IGVFFI6587BAHX](/sequence-files/IGVFFI6587BAHX/), [IGVFFI1954VLUX](/sequence-files/IGVFFI1954VLUX/) 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": "/measurement-sets/IGVFDS9384BVGM/"
}
]
},
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{
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"aliases": [
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],
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}
],
"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": "2023-12-08T23:53:40.208996+00:00",
"donors": [
{
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"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
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},
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],
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"term_name": "Illumina NextSeq 2000"
},
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"upload_status": "validated"
},
{
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],
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},
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"upload_status": "validated"
},
{
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"accession": "IGVFFI4547PKAZ",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane1_seqlane1_I2"
],
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"file_format": "fastq",
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"href": "/sequence-files/IGVFFI4547PKAZ/@@download/IGVFFI4547PKAZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/9cc9750f-24b9-431b-914c-c4fe9e284f56/IGVFFI4547PKAZ.fastq.gz",
"sequencing_platform": {
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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/exprs_1/exprs_1_S1_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9410BUAR/",
"accession": "IGVFFI9410BUAR",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane1_seqlane1_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:34.011893+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI9410BUAR/@@download/IGVFFI9410BUAR.fastq.gz",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1249MWVF/",
"accession": "IGVFFI1249MWVF",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane1_seqlane1_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:31.799354+00:00",
"file_format": "fastq",
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"term_name": "Illumina NextSeq 2000"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6587BAHX/",
"accession": "IGVFFI6587BAHX",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane1_seqlane2_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:38.457772+00:00",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1954VLUX/",
"accession": "IGVFFI1954VLUX",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane1_seqlane2_R2"
],
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"creation_timestamp": "2023-12-09T00:51:39.598659+00:00",
"file_format": "fastq",
"file_size": 4837591546,
"href": "/sequence-files/IGVFFI1954VLUX/@@download/IGVFFI1954VLUX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/ec219ad7-a994-4851-9e87-c13896bc334b/IGVFFI1954VLUX.fastq.gz",
"sequencing_platform": {
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"term_name": "Illumina NextSeq 2000"
},
"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/exprs_1/exprs_1_S1_L002_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_file_set_for": [
"/analysis-sets/IGVFDS4021XJLW/"
],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"notes": "The readout 86015c12-b9a6-43ba-9601-5d75aab4d39c was removed from this measurement set. This measurement set previously did not specify a preferred_assay_title, but the property is now required so it has been defaulted to SUPERSTARR. Please update with an appropriate preferred_assay_title.",
"preferred_assay_title": "scCRISPR screen",
"protocols": [
"https://www.protocols.io/view/methods-from-multiplex-single-cell-crispra-screeni-c5zvy766"
],
"publications": [
{
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"publication_identifiers": [
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]
}
],
"release_timestamp": "2024-08-13T20:47:21.069761+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7750SNNY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7750SNNY",
"aliases": [
"jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane1"
],
"cell_fate_change_treatments": [
{
"@id": "/treatments/13a2bfe2-9124-4254-b0fe-8c221077201f/",
"purpose": "differentiation",
"summary": "Treatment of 2 μg/mL doxycycline hyclate",
"treatment_type": "chemical"
}
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS7581DNXF/",
"accession": "IGVFDS7581DNXF",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci"
}
],
"modifications": [
{
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"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: 10Xlane1), male, Homo sapiens modified with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000540/",
"term_name": "neuron"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "21",
"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": "scCRISPR activation screen integrating a guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci",
"uuid": "6eece0f5-d172-4615-ac08-40151c695c52"
}