{
"@context": "/terms/",
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"MeasurementSet",
"FileSet",
"Item"
],
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"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane2_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 [IGVFDS2220HHTN](/auxiliary-sets/IGVFDS2220HHTN/) has sequence file(s): [IGVFFI4137IEHI](/sequence-files/IGVFFI4137IEHI/), [IGVFFI4398ITZJ](/sequence-files/IGVFFI4398ITZJ/), [IGVFFI4961EMLW](/sequence-files/IGVFFI4961EMLW/), [IGVFFI7687RJYL](/sequence-files/IGVFFI7687RJYL/), [IGVFFI7842UOGS](/sequence-files/IGVFFI7842UOGS/), [IGVFFI4732FLWG](/sequence-files/IGVFFI4732FLWG/), [IGVFFI8008YPNQ](/sequence-files/IGVFFI8008YPNQ/), [IGVFFI0849UBQW](/sequence-files/IGVFFI0849UBQW/) 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/IGVFDS2220HHTN/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0272VVTX](/measurement-sets/IGVFDS0272VVTX/) has sequence file(s): [IGVFFI1419AQFC](/sequence-files/IGVFFI1419AQFC/), [IGVFFI9667UEYM](/sequence-files/IGVFFI9667UEYM/), [IGVFFI6374XWBH](/sequence-files/IGVFFI6374XWBH/), [IGVFFI2239NJFO](/sequence-files/IGVFFI2239NJFO/), [IGVFFI5160NESU](/sequence-files/IGVFFI5160NESU/), [IGVFFI4890DZGD](/sequence-files/IGVFFI4890DZGD/), [IGVFFI6684VWOI](/sequence-files/IGVFFI6684VWOI/), [IGVFFI2130NYWI](/sequence-files/IGVFFI2130NYWI/) 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/IGVFDS0272VVTX/"
}
]
},
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{
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"accession": "IGVFDS2220HHTN",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane2_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": "2023-12-08T23:53:41.149085+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",
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{
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"aliases": [
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],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:41.879729+00:00",
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"file_size": 642095184,
"href": "/sequence-files/IGVFFI1419AQFC/@@download/IGVFFI1419AQFC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/879a5e4e-7d37-499f-8f1b-d3385698969b/IGVFFI1419AQFC.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_2/exprs_2_S2_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9667UEYM/",
"accession": "IGVFFI9667UEYM",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane2_seqlane1_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:40.696835+00:00",
"file_format": "fastq",
"file_size": 580968707,
"href": "/sequence-files/IGVFFI9667UEYM/@@download/IGVFFI9667UEYM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/6058fc55-2957-4040-97be-9a64d19b3205/IGVFFI9667UEYM.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_2/exprs_2_S2_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6374XWBH/",
"accession": "IGVFFI6374XWBH",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane2_seqlane1_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:42.953663+00:00",
"file_format": "fastq",
"file_size": 2104263570,
"href": "/sequence-files/IGVFFI6374XWBH/@@download/IGVFFI6374XWBH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/fd5a8469-0aa3-467e-b17b-1acba11cbdcf/IGVFFI6374XWBH.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_2/exprs_2_S2_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2239NJFO/",
"accession": "IGVFFI2239NJFO",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane2_seqlane1_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:44.026255+00:00",
"file_format": "fastq",
"file_size": 4742060984,
"href": "/sequence-files/IGVFFI2239NJFO/@@download/IGVFFI2239NJFO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/a80ace72-5e9c-4c63-94db-c54c002b320f/IGVFFI2239NJFO.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_2/exprs_2_S2_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5160NESU/",
"accession": "IGVFFI5160NESU",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane2_seqlane2_I2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:46.182804+00:00",
"file_format": "fastq",
"file_size": 615851288,
"href": "/sequence-files/IGVFFI5160NESU/@@download/IGVFFI5160NESU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/ff5b9f4c-4b34-4c0f-9a82-d01e60d51ec3/IGVFFI5160NESU.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_2/exprs_2_S2_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4890DZGD/",
"accession": "IGVFFI4890DZGD",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane2_seqlane2_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:47.241894+00:00",
"file_format": "fastq",
"file_size": 2046002093,
"href": "/sequence-files/IGVFFI4890DZGD/@@download/IGVFFI4890DZGD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/11e25bee-3a6e-49d7-a02f-21a16a3dd1bd/IGVFFI4890DZGD.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_2/exprs_2_S2_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6684VWOI/",
"accession": "IGVFFI6684VWOI",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane2_seqlane2_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:48.487783+00:00",
"file_format": "fastq",
"file_size": 4561708975,
"href": "/sequence-files/IGVFFI6684VWOI/@@download/IGVFFI6684VWOI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/9faf792b-fb60-47a3-9723-663a4b2d47ba/IGVFFI6684VWOI.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_2/exprs_2_S2_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2130NYWI/",
"accession": "IGVFFI2130NYWI",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane2_seqlane2_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:45.146940+00:00",
"file_format": "fastq",
"file_size": 558519381,
"href": "/sequence-files/IGVFFI2130NYWI/@@download/IGVFFI2130NYWI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/93c55a42-fae1-41fa-b81d-206c49fb1895/IGVFFI2130NYWI.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_2/exprs_2_S2_L002_I1_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": "2024-08-13T20:47:22.196305+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9913PXTT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9913PXTT",
"aliases": [
"jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane2"
],
"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: 10Xlane2), 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": "2023-12-09T00:51:03.848506+00:00",
"summary": "scCRISPR activation screen integrating a guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci",
"uuid": "e44c57f5-8f0c-40dd-966d-944b1812fbbb"
}