{
"@context": "/terms/",
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"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2385QENN",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane3_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 [IGVFDS2532AVSC](/auxiliary-sets/IGVFDS2532AVSC/) has sequence file(s): [IGVFFI5740EZRO](/sequence-files/IGVFFI5740EZRO/), [IGVFFI5101XXFL](/sequence-files/IGVFFI5101XXFL/), [IGVFFI2904WAAT](/sequence-files/IGVFFI2904WAAT/), [IGVFFI7440JFKZ](/sequence-files/IGVFFI7440JFKZ/), [IGVFFI3911GHFM](/sequence-files/IGVFFI3911GHFM/), [IGVFFI4073XXVS](/sequence-files/IGVFFI4073XXVS/), [IGVFFI8818WFVA](/sequence-files/IGVFFI8818WFVA/), [IGVFFI3761PGKJ](/sequence-files/IGVFFI3761PGKJ/) 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/IGVFDS2532AVSC/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2385QENN](/measurement-sets/IGVFDS2385QENN/) has sequence file(s): [IGVFFI2611VQUT](/sequence-files/IGVFFI2611VQUT/), [IGVFFI0983CKVR](/sequence-files/IGVFFI0983CKVR/), [IGVFFI7407CDAT](/sequence-files/IGVFFI7407CDAT/), [IGVFFI4517FSHP](/sequence-files/IGVFFI4517FSHP/), [IGVFFI8009AYNA](/sequence-files/IGVFFI8009AYNA/), [IGVFFI6618WYLI](/sequence-files/IGVFFI6618WYLI/), [IGVFFI2702LBCH](/sequence-files/IGVFFI2702LBCH/), [IGVFFI0113PKVX](/sequence-files/IGVFFI0113PKVX/) 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/IGVFDS2385QENN/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2532AVSC/",
"accession": "IGVFDS2532AVSC",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane3_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": "2023-12-08T23:53:42.157326+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [
{
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"accession": "IGVFFI2611VQUT",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane3_seqlane1_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:53.374162+00:00",
"file_format": "fastq",
"file_size": 5280792069,
"href": "/sequence-files/IGVFFI2611VQUT/@@download/IGVFFI2611VQUT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/a3c88edd-3777-4b61-b699-bb5c4822b9dd/IGVFFI2611VQUT.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/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/exprs_3/exprs_3_S3_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0983CKVR/",
"accession": "IGVFFI0983CKVR",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane3_seqlane1_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:49.700747+00:00",
"file_format": "fastq",
"file_size": 746687808,
"href": "/sequence-files/IGVFFI0983CKVR/@@download/IGVFFI0983CKVR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/7884fd32-d501-4cd0-bdc4-7167981d1e02/IGVFFI0983CKVR.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/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/exprs_3/exprs_3_S3_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7407CDAT/",
"accession": "IGVFFI7407CDAT",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane3_seqlane1_I2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:50.836281+00:00",
"file_format": "fastq",
"file_size": 701068245,
"href": "/sequence-files/IGVFFI7407CDAT/@@download/IGVFFI7407CDAT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/747cfd59-e881-458f-a104-a0580a7fedfd/IGVFFI7407CDAT.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/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/exprs_3/exprs_3_S3_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4517FSHP/",
"accession": "IGVFFI4517FSHP",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane3_seqlane1_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:52.026929+00:00",
"file_format": "fastq",
"file_size": 2344688789,
"href": "/sequence-files/IGVFFI4517FSHP/@@download/IGVFFI4517FSHP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/897968af-c773-4bd8-8a1e-cd57d69fe1cd/IGVFFI4517FSHP.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/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/exprs_3/exprs_3_S3_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8009AYNA/",
"accession": "IGVFFI8009AYNA",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane3_seqlane2_I2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:55.831368+00:00",
"file_format": "fastq",
"file_size": 655306179,
"href": "/sequence-files/IGVFFI8009AYNA/@@download/IGVFFI8009AYNA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/982e54e2-f65a-4216-8886-e24054ac64e2/IGVFFI8009AYNA.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/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/exprs_3/exprs_3_S3_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6618WYLI/",
"accession": "IGVFFI6618WYLI",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane3_seqlane2_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:56.991098+00:00",
"file_format": "fastq",
"file_size": 2267925104,
"href": "/sequence-files/IGVFFI6618WYLI/@@download/IGVFFI6618WYLI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/4a05d15b-8c44-4e80-ae9f-93732a37b9c1/IGVFFI6618WYLI.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/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/exprs_3/exprs_3_S3_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2702LBCH/",
"accession": "IGVFFI2702LBCH",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane3_seqlane2_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:54.505814+00:00",
"file_format": "fastq",
"file_size": 702793401,
"href": "/sequence-files/IGVFFI2702LBCH/@@download/IGVFFI2702LBCH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/42fae64f-916c-41d8-aa49-799745f801e6/IGVFFI2702LBCH.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/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/exprs_3/exprs_3_S3_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0113PKVX/",
"accession": "IGVFFI0113PKVX",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane3_seqlane2_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:58.179366+00:00",
"file_format": "fastq",
"file_size": 5060093558,
"href": "/sequence-files/IGVFFI0113PKVX/@@download/IGVFFI0113PKVX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/1d5b5050-fc30-482c-8061-f64e4e1345f9/IGVFFI0113PKVX.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/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/exprs_3/exprs_3_S3_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": [
{
"@id": "/publications/20fcbdbb-5a47-41c6-b80b-e6dd0e8a8d3e/",
"publication_identifiers": [
"doi:10.1101/2023.03.28.534017"
]
}
],
"release_timestamp": "2024-08-13T20:47:21.859213+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8317ZTFV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8317ZTFV",
"aliases": [
"jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane3"
],
"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": [
{
"@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: 10Xlane3), 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": "2023-12-09T00:51:13.101456+00:00",
"summary": "scCRISPR activation screen integrating a guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci",
"uuid": "ee12fd85-d813-46d6-a37c-c21a420bcc0a"
}