{
"@context": "/terms/",
"@id": "/construct-library-sets/IGVFDS2302LCEO/",
"@type": [
"ConstructLibrarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS2302LCEO",
"aliases": [
"gary-hon:TF_Perturb_seq_Pilot_sgRNA_list"
],
"applied_to_samples": [
{
"@id": "/in-vitro-systems/IGVFSM6351SIZQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6351SIZQ",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti"
],
"classifications": [
"differentiated cell specimen"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days, male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
}
},
{
"@id": "/in-vitro-systems/IGVFSM9036LWJT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9036LWJT",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti"
],
"classifications": [
"differentiated cell specimen"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to neural stem cell for 20 days, male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000047/",
"status": "preview",
"term_name": "neural stem cell"
}
},
{
"@id": "/in-vitro-systems/IGVFSM7513BJDT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7513BJDT",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti_LW277"
],
"classifications": [
"differentiated cell specimen"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW277), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
}
},
{
"@id": "/in-vitro-systems/IGVFSM7499ZWUW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7499ZWUW",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti_LW278"
],
"classifications": [
"differentiated cell specimen"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW278), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
}
},
{
"@id": "/in-vitro-systems/IGVFSM0559UNMK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0559UNMK",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti_LW279"
],
"classifications": [
"differentiated cell specimen"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW279), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
}
},
{
"@id": "/in-vitro-systems/IGVFSM0604KDJF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0604KDJF",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti_LW280"
],
"classifications": [
"differentiated cell specimen"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW280), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
}
},
{
"@id": "/in-vitro-systems/IGVFSM0956HKRJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0956HKRJ",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW281"
],
"classifications": [
"differentiated cell specimen"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to neural stem cell for 20 days (cellular sub pool: subpool_LW281), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000047/",
"status": "preview",
"term_name": "neural stem cell"
}
},
{
"@id": "/in-vitro-systems/IGVFSM1288TQKF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1288TQKF",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW282"
],
"classifications": [
"differentiated cell specimen"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to neural stem cell for 20 days (cellular sub pool: subpool_LW282), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000047/",
"status": "preview",
"term_name": "neural stem cell"
}
},
{
"@id": "/in-vitro-systems/IGVFSM8464JMJS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8464JMJS",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW283"
],
"classifications": [
"differentiated cell specimen"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to neural stem cell for 20 days (cellular sub pool: subpool_LW283), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000047/",
"status": "preview",
"term_name": "neural stem cell"
}
},
{
"@id": "/in-vitro-systems/IGVFSM2597WGYB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2597WGYB",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_NPC_Lenti_LW284"
],
"classifications": [
"differentiated cell specimen"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to neural stem cell for 20 days (cellular sub pool: subpool_LW284), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000047/",
"status": "preview",
"term_name": "neural stem cell"
}
},
{
"@id": "/in-vitro-systems/IGVFSM2726ORRN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2726ORRN",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW286"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) cell line (cellular sub pool: subpool_LW286), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM9411HZLU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9411HZLU",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW288"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) cell line (cellular sub pool: subpool_LW288), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM1153INDY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1153INDY",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW287"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) cell line (cellular sub pool: subpool_LW287), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM1597KVRS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1597KVRS",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti_LW289"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) cell line (cellular sub pool: subpool_LW289), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library"
},
{
"@id": "/in-vitro-systems/IGVFSM5481HUWA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5481HUWA",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_iPSC_Lenti"
],
"classifications": [
"cell line"
],
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"status": "released",
"taxa": "Homo sapiens"
}
],
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "preview",
"summary": "GM25256 (WTC-11) cell line, male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library"
}
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview construct library set [IGVFDS2302LCEO](/construct-library-sets/IGVFDS2302LCEO/) has in progress subobject tabular file [IGVFFI7568FEHI](/tabular-files/IGVFFI7568FEHI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/construct-library-sets/IGVFDS2302LCEO/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing plasmid map",
"detail": "Construct library set [IGVFDS2302LCEO](/construct-library-sets/IGVFDS2302LCEO/) does not have a plasmid map attached in `documents`. Construct library sets are expected to be associated with a plasmid map document.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_construct_library_set_plasmid_map",
"path": "/construct-library-sets/IGVFDS2302LCEO/"
}
],
"WARNING": [
{
"category": "missing files",
"detail": "Construct library set [IGVFDS2302LCEO](/construct-library-sets/IGVFDS2302LCEO/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/construct-library-sets/IGVFDS2302LCEO/"
}
]
},
"award": {
"@id": "/awards/HG011996/",
"component": "functional characterization"
},
"control_for": [],
"creation_timestamp": "2024-02-21T20:26:25.260141+00:00",
"description": "sgRNA reverse compliment sequences used for FBA sgRNA mapping. Loci list will be updated, but currently all the loci can be extracted from the sgRNA file. Reach out to the the Hon Lab for any further questions",
"file_set_type": "guide library",
"files": [],
"guide_type": "sgRNA",
"input_for": [],
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI7568FEHI/",
"accession": "IGVFFI7568FEHI",
"aliases": [
"gary-hon:TF_Perturbseq_Pilot_sgRNA_file"
],
"content_type": "guide RNA sequences",
"file_format": "tsv",
"status": "in progress",
"upload_status": "invalidated"
}
],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"large_scale_loci_list": {
"@id": "/tabular-files/IGVFFI7568FEHI/",
"accession": "IGVFFI7568FEHI",
"aliases": [
"gary-hon:TF_Perturbseq_Pilot_sgRNA_file"
],
"status": "in progress"
},
"schema_version": "10",
"scope": "loci",
"selection_criteria": [
"accessible genome regions"
],
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitter_comment": "sgRNA reverse compliment sequences used for FBA sgRNA mapping. Loci list will be updated, but currently all the loci can be extracted from the sgRNA file. Reach out to the the Hon Lab for any further questions",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"uuid": "b9b13358-ad6a-4ed9-acf3-5b93a71c504e"
}