{
"@context": "/terms/",
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"AuxiliarySet",
"FileSet",
"Item"
],
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],
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{
"category": "missing publication",
"detail": "Auxiliary set [IGVFDS9860EXKL](/auxiliary-sets/IGVFDS9860EXKL/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/auxiliary-sets/IGVFDS9860EXKL/"
},
{
"category": "NTR term ID",
"detail": "Sample term for [NTR_0000753](/sample-terms/NTR_0000753/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
"path": "/sample-terms/NTR_0000753/"
},
{
"category": "missing publication",
"detail": "Multiplexed sample [IGVFSM3646QLDO](/multiplexed-samples/IGVFSM3646QLDO/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/multiplexed-samples/IGVFSM3646QLDO/"
}
]
},
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"title": "Ansuman Satpathy"
},
"title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
},
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"creation_timestamp": "2024-07-19T22:07:59.488577+00:00",
"data_use_limitation_summaries": [
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],
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{
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"aliases": [
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],
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"status": "released",
"taxa": "Homo sapiens"
}
],
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],
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},
{
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],
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"href": "/sequence-files/IGVFFI9650KYBD/@@download/IGVFFI9650KYBD.fastq.gz",
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"upload_status": "validated"
},
{
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"aliases": [
"ansuman-satpathy:igvf_exp2_multi_10x1_NGS2_r1"
],
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"controlled_access": false,
"creation_timestamp": "2024-07-21T22:33:25.835891+00:00",
"file_format": "fastq",
"file_size": 654195032,
"href": "/sequence-files/IGVFFI0210PZLR/@@download/IGVFFI0210PZLR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/21/8f4b1d2c-f2c8-470f-950e-c3f5d95ad7aa/IGVFFI0210PZLR.fastq.gz",
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},
{
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],
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"href": "/sequence-files/IGVFFI8387TIGP/@@download/IGVFFI8387TIGP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/21/07956cf1-3726-451c-b03f-13cf5fbd3256/IGVFFI8387TIGP.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6392OPMO/",
"accession": "IGVFFI6392OPMO",
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],
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"controlled_access": false,
"creation_timestamp": "2024-07-21T22:28:21.989663+00:00",
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"file_size": 657185450,
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8462BKYM/",
"accession": "IGVFFI8462BKYM",
"aliases": [
"ansuman-satpathy:igvf_exp2_multi_10x1_NGS1_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T22:33:10.007757+00:00",
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"file_size": 240475515,
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"s3_uri": "s3://igvf-files/2024/07/21/f51bdfd9-556f-41d0-89c7-431caba90b4c/IGVFFI8462BKYM.fastq.gz",
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"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8702MWTF/",
"accession": "IGVFFI8702MWTF",
"aliases": [
"ansuman-satpathy:igvf_exp2_multi_10x1_NGS2_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T22:33:47.525486+00:00",
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"file_size": 239168165,
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"s3_uri": "s3://igvf-files/2024/07/21/4ae9c2dd-d918-4b09-aa98-2c225b17ad91/IGVFFI8702MWTF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0022840/",
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0292SYVB/",
"accession": "IGVFFI0292SYVB",
"aliases": [
"ansuman-satpathy:igvf_exp2_multi_10x1_NGS1_i2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-21T22:33:17.345596+00:00",
"file_format": "fastq",
"file_size": 200901369,
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"s3_uri": "s3://igvf-files/2024/07/21/fa1203ec-2608-4218-a6bc-8f60258b19eb/IGVFFI0292SYVB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0022840/",
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"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230522_IGVF2_McGinnis/MULTI/FASTQ/MULTI_3_S46_L007_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9398JPQS/",
"accession": "IGVFFI9398JPQS",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp2_multi_10x1_NGS2"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:35:47.845141+00:00",
"file_format": "yaml",
"file_size": 1335,
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"s3_uri": "s3://igvf-files/2024/09/18/832daf49-34a6-425a-b963-e8e551f38064/IGVFFI9398JPQS.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp2_multi_10x1_NGS2_multi_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4120EDXM/",
"accession": "IGVFFI4120EDXM",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp2_multi_10x1_NGS1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:35:44.452698+00:00",
"file_format": "yaml",
"file_size": 1338,
"href": "/configuration-files/IGVFFI4120EDXM/@@download/IGVFFI4120EDXM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/df5f3cce-3894-4c2f-8745-46e62da3453b/IGVFFI4120EDXM.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp2_multi_10x1_NGS1_multi_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1583PWNS/"
],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS5111SPGA/",
"accession": "IGVFDS5111SPGA",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf2_10x1"
],
"preferred_assay_title": "10x multiome with MULTI-seq",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6369SLCB/",
"accession": "IGVFDS6369SLCB",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf2_10x1"
],
"preferred_assay_title": "10x multiome with MULTI-seq",
"status": "released"
}
],
"notes": "File_set_type enum oligo-conjugated lipids has been renamed to be lipid-conjugated oligo sequencing.",
"release_timestamp": "2025-03-07T01:10:41.797575+00:00",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM3646QLDO/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM3646QLDO",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf2_10x1"
],
"classifications": [
"cell line",
"multiplexed sample"
],
"disease_terms": [],
"institutional_certificates": [
{
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"certificate_identifier": "IP115-16",
"controlled_access": false,
"status": "released"
}
],
"modifications": [],
"sample_terms": [
{
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"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:TeloHAEC"
],
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"summary": "TeloHAEC",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (female) TeloHAEC cell line treated with 10 ng/mL tumor necrosis factor alpha for 4 hours; Homo sapiens (female) TeloHAEC cell line; ... and 7 more samples",
"taxa": "Homo sapiens",
"treatments": [
{
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},
{
"@id": "/treatments/de8a9e87-d0e1-4ecb-bc9d-08e61b4ff368/",
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"status": "in progress",
"summary": "Treatment of 10 ng/mL tumor necrosis factor alpha for 1 day",
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}
]
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
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"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2024-07-21T22:28:21.989663+00:00",
"summary": "lipid-conjugated oligo sequencing for single-nucleus RNA sequencing assay (10x multiome with MULTI-seq), single-nucleus ATAC-seq (10x multiome with MULTI-seq)",
"uuid": "4f8daf54-161f-4da7-bf37-22d060a6d8ca"
}