{
"@context": "/terms/",
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"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4863BMGZ",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane1_exprs"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003660/",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4863BMGZ](/measurement-sets/IGVFDS4863BMGZ/) has sequence file(s): [IGVFFI5073SNLU](/sequence-files/IGVFFI5073SNLU/), [IGVFFI5106LXXU](/sequence-files/IGVFFI5106LXXU/), [IGVFFI6599UWGY](/sequence-files/IGVFFI6599UWGY/), [IGVFFI0072NENY](/sequence-files/IGVFFI0072NENY/), [IGVFFI3105RHFR](/sequence-files/IGVFFI3105RHFR/), [IGVFFI8326SURF](/sequence-files/IGVFFI8326SURF/) 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/IGVFDS4863BMGZ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4502LQQH](/auxiliary-sets/IGVFDS4502LQQH/) has sequence file(s): [IGVFFI9764UXRA](/sequence-files/IGVFFI9764UXRA/), [IGVFFI7570AUYM](/sequence-files/IGVFFI7570AUYM/), [IGVFFI3927QEMS](/sequence-files/IGVFFI3927QEMS/), [IGVFFI4648IIPG](/sequence-files/IGVFFI4648IIPG/), [IGVFFI3189OKPU](/sequence-files/IGVFFI3189OKPU/), [IGVFFI1733REWQ](/sequence-files/IGVFFI1733REWQ/) 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/IGVFDS4502LQQH/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4502LQQH/",
"accession": "IGVFDS4502LQQH",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_10Xlane1_CS1"
],
"file_set_type": "gRNA sequencing"
}
],
"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": "2023-12-08T23:53:36.807086+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"accession": "IGVFDO9208RPQQ",
"aliases": [
"igvf:donor_of_K562"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI5073SNLU/",
"accession": "IGVFFI5073SNLU",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_exprs_10Xlane1_seqlane2_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:13.802089+00:00",
"file_format": "fastq",
"file_size": 793151105,
"href": "/sequence-files/IGVFFI5073SNLU/@@download/IGVFFI5073SNLU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/a0dac823-6212-4758-aebf-ccc43ddc77bc/IGVFFI5073SNLU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"term_name": "Illumina NextSeq 2000"
},
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/K562_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAHG2HHV/VP64_exprs_1/VP64_exprs_1_S1_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5106LXXU/",
"accession": "IGVFFI5106LXXU",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_exprs_10Xlane1_seqlane1_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:12.513274+00:00",
"file_format": "fastq",
"file_size": 5767958513,
"href": "/sequence-files/IGVFFI5106LXXU/@@download/IGVFFI5106LXXU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/bb0dd376-a44c-4cc9-ba76-ed0f84869874/IGVFFI5106LXXU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"term_name": "Illumina NextSeq 2000"
},
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/K562_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAHG2HHV/VP64_exprs_1/VP64_exprs_1_S1_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6599UWGY/",
"accession": "IGVFFI6599UWGY",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_exprs_10Xlane1_seqlane2_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:16.323590+00:00",
"file_format": "fastq",
"file_size": 5816287410,
"href": "/sequence-files/IGVFFI6599UWGY/@@download/IGVFFI6599UWGY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/23cfe933-3797-41bc-ab2e-6ac48ddcdb5c/IGVFFI6599UWGY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"term_name": "Illumina NextSeq 2000"
},
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/K562_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAHG2HHV/VP64_exprs_1/VP64_exprs_1_S1_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0072NENY/",
"accession": "IGVFFI0072NENY",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_exprs_10Xlane1_seqlane1_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:09.539804+00:00",
"file_format": "fastq",
"file_size": 812388447,
"href": "/sequence-files/IGVFFI0072NENY/@@download/IGVFFI0072NENY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/fe3649d9-1f1d-4dbe-aa29-1b113131d9f2/IGVFFI0072NENY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"term_name": "Illumina NextSeq 2000"
},
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/K562_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAHG2HHV/VP64_exprs_1/VP64_exprs_1_S1_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3105RHFR/",
"accession": "IGVFFI3105RHFR",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_exprs_10Xlane1_seqlane1_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:11.213594+00:00",
"file_format": "fastq",
"file_size": 2684213036,
"href": "/sequence-files/IGVFFI3105RHFR/@@download/IGVFFI3105RHFR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/ef8ca8bd-9911-4ba6-98df-e6608f72d38d/IGVFFI3105RHFR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"term_name": "Illumina NextSeq 2000"
},
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/K562_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAHG2HHV/VP64_exprs_1/VP64_exprs_1_S1_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8326SURF/",
"accession": "IGVFFI8326SURF",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VP64_sequence_exprs_10Xlane1_seqlane2_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:15.060294+00:00",
"file_format": "fastq",
"file_size": 2726298770,
"href": "/sequence-files/IGVFFI8326SURF/@@download/IGVFFI8326SURF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/e23bcfbf-adba-4923-9b51-53c1a4de97db/IGVFFI8326SURF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"term_name": "Illumina NextSeq 2000"
},
"submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/K562_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAHG2HHV/VP64_exprs_1/VP64_exprs_1_S1_L002_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_file_set_for": [
"/analysis-sets/IGVFDS9078ZWQH/"
],
"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": [
{
"@id": "/publications/20fcbdbb-5a47-41c6-b80b-e6dd0e8a8d3e/",
"publication_identifiers": [
"doi:10.1101/2023.03.28.534017"
]
}
],
"release_timestamp": "2024-08-13T20:47:07.511463+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4521QSSO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4521QSSO",
"aliases": [
"jay-shendure:CRISPRa_VP64_K562_10Xlane1"
],
"classifications": [
"cell line"
],
"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": [
{
"@id": "/crispr-modifications/ee99bf66-2a5a-4ec6-8380-9434b259afd1/",
"modality": "activation"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:K562"
],
"status": "released",
"summary": "K562",
"term_name": "K562"
}
],
"status": "released",
"summary": "K562 cell line (cellular sub pool: 10Xlane1), female, Homo sapiens modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "21",
"status": "released",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"submitted_files_timestamp": "2023-12-09T00:49:53.541322+00:00",
"summary": "scCRISPR activation screen integrating a guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci",
"uuid": "4b1872ed-da59-488b-ad5c-b5ff2a763a76"
}