{
"@context": "/terms/",
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"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2133JAFB",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane4_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 [IGVFDS2133JAFB](/measurement-sets/IGVFDS2133JAFB/) has sequence file(s): [IGVFFI2659ZSIM](/sequence-files/IGVFFI2659ZSIM/), [IGVFFI4323HGFN](/sequence-files/IGVFFI4323HGFN/), [IGVFFI8572PBWR](/sequence-files/IGVFFI8572PBWR/), [IGVFFI7653WTAT](/sequence-files/IGVFFI7653WTAT/), [IGVFFI5581RKRW](/sequence-files/IGVFFI5581RKRW/), [IGVFFI4172XVXM](/sequence-files/IGVFFI4172XVXM/), [IGVFFI4882IDVE](/sequence-files/IGVFFI4882IDVE/), [IGVFFI8871JYFX](/sequence-files/IGVFFI8871JYFX/) 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/IGVFDS2133JAFB/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7598WPXV](/auxiliary-sets/IGVFDS7598WPXV/) has sequence file(s): [IGVFFI7501QBYI](/sequence-files/IGVFFI7501QBYI/), [IGVFFI3432JHMF](/sequence-files/IGVFFI3432JHMF/), [IGVFFI8644VEVN](/sequence-files/IGVFFI8644VEVN/), [IGVFFI1501KPWU](/sequence-files/IGVFFI1501KPWU/), [IGVFFI7243XYXN](/sequence-files/IGVFFI7243XYXN/), [IGVFFI5101PVJN](/sequence-files/IGVFFI5101PVJN/), [IGVFFI5318WDGT](/sequence-files/IGVFFI5318WDGT/), [IGVFFI2675LZFM](/sequence-files/IGVFFI2675LZFM/) 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/IGVFDS7598WPXV/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7598WPXV/",
"accession": "IGVFDS7598WPXV",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_10Xlane4_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": "2023-12-08T23:53:42.815615+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": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane4_seqlane1_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:52:03.899860+00:00",
"file_format": "fastq",
"file_size": 7521619215,
"href": "/sequence-files/IGVFFI2659ZSIM/@@download/IGVFFI2659ZSIM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/6f199754-3a28-4844-91c9-650671d72ee6/IGVFFI2659ZSIM.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_4/exprs_4_S4_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4323HGFN/",
"accession": "IGVFFI4323HGFN",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane4_seqlane2_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:52:08.840175+00:00",
"file_format": "fastq",
"file_size": 7255273038,
"href": "/sequence-files/IGVFFI4323HGFN/@@download/IGVFFI4323HGFN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/a52ca7bc-6af7-48ee-9759-3dc3f57d363e/IGVFFI4323HGFN.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_4/exprs_4_S4_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8572PBWR/",
"accession": "IGVFFI8572PBWR",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane4_seqlane2_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:52:05.079631+00:00",
"file_format": "fastq",
"file_size": 867252310,
"href": "/sequence-files/IGVFFI8572PBWR/@@download/IGVFFI8572PBWR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/5d84c18f-a36f-4802-b26a-7f6f01911e07/IGVFFI8572PBWR.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_4/exprs_4_S4_L002_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7653WTAT/",
"accession": "IGVFFI7653WTAT",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane4_seqlane1_I1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:51:59.463169+00:00",
"file_format": "fastq",
"file_size": 921615464,
"href": "/sequence-files/IGVFFI7653WTAT/@@download/IGVFFI7653WTAT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/4021aef8-3d64-4c18-a739-6193a60671f3/IGVFFI7653WTAT.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_4/exprs_4_S4_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5581RKRW/",
"accession": "IGVFFI5581RKRW",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane4_seqlane1_I2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:52:00.647852+00:00",
"file_format": "fastq",
"file_size": 907355368,
"href": "/sequence-files/IGVFFI5581RKRW/@@download/IGVFFI5581RKRW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/2c466b30-6f00-453e-94a6-76f984cb2645/IGVFFI5581RKRW.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_4/exprs_4_S4_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4172XVXM/",
"accession": "IGVFFI4172XVXM",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane4_seqlane1_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:52:02.520361+00:00",
"file_format": "fastq",
"file_size": 3269425316,
"href": "/sequence-files/IGVFFI4172XVXM/@@download/IGVFFI4172XVXM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/4b1abb0b-26ae-43b4-bf98-14a0d5a4c944/IGVFFI4172XVXM.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_4/exprs_4_S4_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4882IDVE/",
"accession": "IGVFFI4882IDVE",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane4_seqlane2_I2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:52:06.261825+00:00",
"file_format": "fastq",
"file_size": 842676036,
"href": "/sequence-files/IGVFFI4882IDVE/@@download/IGVFFI4882IDVE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/a851af4a-df41-4d6f-b0bf-18fdc08b4bbc/IGVFFI4882IDVE.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_4/exprs_4_S4_L002_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8871JYFX/",
"accession": "IGVFFI8871JYFX",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane4_seqlane2_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:52:07.600402+00:00",
"file_format": "fastq",
"file_size": 3185752510,
"href": "/sequence-files/IGVFFI8871JYFX/@@download/IGVFFI8871JYFX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/21903bd5-9962-4cd6-9423-8a849487e100/IGVFFI8871JYFX.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_4/exprs_4_S4_L002_R1_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": "2024-08-13T20:47:22.997373+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8382KOXO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8382KOXO",
"aliases": [
"jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_10Xlane4"
],
"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: 10Xlane4), 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": "2023-12-09T00:51:21.993678+00:00",
"summary": "scCRISPR activation screen integrating a guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci",
"uuid": "7ef1a019-1ec3-47a4-be6e-829b5076481d"
}