{
"@context": "/terms/",
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"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7395DPAD",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_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": "Auxiliary set [IGVFDS4621HUKP](/auxiliary-sets/IGVFDS4621HUKP/) has sequence file(s): [IGVFFI1163CNBZ](/sequence-files/IGVFFI1163CNBZ/), [IGVFFI3887HQZR](/sequence-files/IGVFFI3887HQZR/), [IGVFFI3175HZHT](/sequence-files/IGVFFI3175HZHT/), [IGVFFI5218FTCG](/sequence-files/IGVFFI5218FTCG/), [IGVFFI7439CGLC](/sequence-files/IGVFFI7439CGLC/), [IGVFFI2138EWHH](/sequence-files/IGVFFI2138EWHH/) 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/IGVFDS4621HUKP/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7395DPAD](/measurement-sets/IGVFDS7395DPAD/) has sequence file(s): [IGVFFI0622BUKC](/sequence-files/IGVFFI0622BUKC/), [IGVFFI0367CCRX](/sequence-files/IGVFFI0367CCRX/), [IGVFFI7393XWDY](/sequence-files/IGVFFI7393XWDY/), [IGVFFI1022LUTK](/sequence-files/IGVFFI1022LUTK/), [IGVFFI7864AXDQ](/sequence-files/IGVFFI7864AXDQ/), [IGVFFI3864UPXH](/sequence-files/IGVFFI3864UPXH/) 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/IGVFDS7395DPAD/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4621HUKP/",
"accession": "IGVFDS4621HUKP",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_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": "2023-12-08T23:53:38.652703+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/IGVFFI0622BUKC/",
"accession": "IGVFFI0622BUKC",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_exprs_10Xlane1_seqlane2_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:42.943814+00:00",
"file_format": "fastq",
"file_size": 760768612,
"href": "/sequence-files/IGVFFI0622BUKC/@@download/IGVFFI0622BUKC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/bb654cfc-142a-4e78-a4c5-6827af0b216c/IGVFFI0622BUKC.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/VPR_exprs_1/VPR_exprs_1_S3_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0367CCRX/",
"accession": "IGVFFI0367CCRX",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_exprs_10Xlane1_seqlane1_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:40.819991+00:00",
"file_format": "fastq",
"file_size": 2478974899,
"href": "/sequence-files/IGVFFI0367CCRX/@@download/IGVFFI0367CCRX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/4b0642ef-e2dd-478c-8d42-aee50545e297/IGVFFI0367CCRX.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/VPR_exprs_1/VPR_exprs_1_S3_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7393XWDY/",
"accession": "IGVFFI7393XWDY",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_exprs_10Xlane1_seqlane1_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:41.832428+00:00",
"file_format": "fastq",
"file_size": 5423115860,
"href": "/sequence-files/IGVFFI7393XWDY/@@download/IGVFFI7393XWDY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/ea9cf9e5-e569-4d27-bc29-9db688871fae/IGVFFI7393XWDY.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/VPR_exprs_1/VPR_exprs_1_S3_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1022LUTK/",
"accession": "IGVFFI1022LUTK",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_exprs_10Xlane1_seqlane2_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:44.048756+00:00",
"file_format": "fastq",
"file_size": 2539068153,
"href": "/sequence-files/IGVFFI1022LUTK/@@download/IGVFFI1022LUTK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/4bf9ac06-fa24-49bb-bf2b-0113e1194b8d/IGVFFI1022LUTK.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/VPR_exprs_1/VPR_exprs_1_S3_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7864AXDQ/",
"accession": "IGVFFI7864AXDQ",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_exprs_10Xlane1_seqlane2_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:45.208467+00:00",
"file_format": "fastq",
"file_size": 5512413731,
"href": "/sequence-files/IGVFFI7864AXDQ/@@download/IGVFFI7864AXDQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/cd5f85bd-d6bb-42c1-9192-76e30e8b7ca9/IGVFFI7864AXDQ.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/VPR_exprs_1/VPR_exprs_1_S3_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3864UPXH/",
"accession": "IGVFFI3864UPXH",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_sequence_exprs_10Xlane1_seqlane1_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:50:39.669784+00:00",
"file_format": "fastq",
"file_size": 749066323,
"href": "/sequence-files/IGVFFI3864UPXH/@@download/IGVFFI3864UPXH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/6f2469af-230d-40bc-b7a6-1718bcf4db03/IGVFFI3864UPXH.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/VPR_exprs_1/VPR_exprs_1_S3_L001_I1_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": "2024-08-13T20:47:08.653956+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1594ZOQH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1594ZOQH",
"aliases": [
"jay-shendure:CRISPRa_VPR_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/8b61bce4-105c-435e-9b32-1c8903566a9b/",
"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": "2023-12-09T00:50:25.812810+00:00",
"summary": "scCRISPR activation screen integrating a guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci",
"uuid": "7bb07c40-13cd-4806-b145-1e7006db88e2"
}