{
"@context": "/terms/",
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],
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],
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{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5403GYDH](/auxiliary-sets/IGVFDS5403GYDH/) has sequence file(s): [IGVFFI2639TNEY](/sequence-files/IGVFFI2639TNEY/), [IGVFFI0508AHMI](/sequence-files/IGVFFI0508AHMI/), [IGVFFI7827HSIX](/sequence-files/IGVFFI7827HSIX/), [IGVFFI1627XZSE](/sequence-files/IGVFFI1627XZSE/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
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"path": "/auxiliary-sets/IGVFDS5403GYDH/"
}
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"title": "Gary Hon"
},
"title": "Multiscale functional characterization of genomic variation in human developmental disorders"
},
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{
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{
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"accession": "IGVFFI9879UTKX",
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"summary": "guide RNA sequences"
}
],
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"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
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"creation_timestamp": "2024-08-16T20:05:16.185953+00:00",
"data_use_limitation_summaries": [
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],
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{
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"aliases": [
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],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
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{
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],
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"creation_timestamp": "2024-11-13T19:47:54.084196+00:00",
"file_format": "fastq",
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"md5sum": "94b6dbf21aeb0a854db1419468cb4967",
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"upload_status": "validated"
},
{
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],
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"creation_timestamp": "2024-11-13T19:46:46.600367+00:00",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7827HSIX/",
"accession": "IGVFFI7827HSIX",
"aliases": [
"gary-hon:LW432B_6_I1"
],
"content_type": "reads",
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"creation_timestamp": "2024-11-13T19:46:12.683418+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI7827HSIX/@@download/IGVFFI7827HSIX.fastq.gz",
"md5sum": "ee7fa81803877a6515350e0df3b6c0bf",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1627XZSE/",
"accession": "IGVFFI1627XZSE",
"aliases": [
"gary-hon:LW432B_6_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-13T19:46:29.086979+00:00",
"file_format": "fastq",
"file_size": 936111968,
"href": "/sequence-files/IGVFFI1627XZSE/@@download/IGVFFI1627XZSE.fastq.gz",
"md5sum": "361f51f2aa3c09da58393ee6c068dd57",
"s3_uri": "s3://igvf-files/2024/11/13/c65146eb-da7c-4c8e-9824-546d2bd5e34d/IGVFFI1627XZSE.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0022841/",
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2024/2024-05-01-Novogene-NovaSeq.Hon19_20/sgRNA//LW432B_S6_L006_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2266YDVM/"
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS8183DTKY/",
"accession": "IGVFDS8183DTKY",
"aliases": [
"gary-hon:differentited_H9_CM_Pilot2_Mini_PB9_LW432"
],
"preferred_assay_title": "Perturb-seq",
"status": "preview"
}
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3839SOTK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3839SOTK",
"aliases": [
"nikhil-munshi:differentited_H9_CM_Pilot2_Mini_PB9_LW432"
],
"cellular_sub_pool": "subpool_LW432",
"classifications": [
"differentiated cell specimen"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0003045/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:H9"
],
"status": "released",
"summary": "H9",
"term_name": "H9"
}
],
"status": "preview",
"summary": "Homo sapiens (female) H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW432) modified with CRISPRi Sp-dCas9, 3 week(s) after transfection with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitted_files_timestamp": "2024-11-13T19:46:12.683418+00:00",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "14a0dd9c-f220-4ef8-b1a7-d75151f6b1c6"
}