{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6521MNHG/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6521MNHG",
"aliases": [
"ansuman-satpathy:multiseq_igvf10_10x2"
],
"audit": {
"INTERNAL_ACTION": [
{
"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/"
}
]
},
"award": {
"@id": "/awards/HG012076/",
"component": "mapping",
"contact_pi": {
"@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
"title": "Ansuman Satpathy"
},
"title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
},
"control_for": [],
"creation_timestamp": "2024-07-22T00:31:30.474154+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO9208RPQQ/",
"accession": "IGVFDO9208RPQQ",
"aliases": [
"igvf:donor_of_K562"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO3459DFTW/",
"accession": "IGVFDO3459DFTW",
"aliases": [
"igvf:donor_of_teloHAEC"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "lipid-conjugated oligo sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI6133ZBWA/",
"accession": "IGVFFI6133ZBWA",
"aliases": [
"ansuman-satpathy:igvf_exp10_multi_10x2_NGS1_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T20:59:54.557458+00:00",
"file_format": "fastq",
"file_size": 547442220,
"href": "/sequence-files/IGVFFI6133ZBWA/@@download/IGVFFI6133ZBWA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/b05c1a73-fb99-4070-a5fb-e658f87b9cb5/IGVFFI6133ZBWA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0022840/",
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230707_IGVF10_McGinnis/MULTI/FASTQ/MULTI_2_CMAS_IGVF10_R_S6_L004_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7897TYMN/",
"accession": "IGVFFI7897TYMN",
"aliases": [
"ansuman-satpathy:igvf_exp10_multi_10x2_NGS2_r1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T21:00:34.121866+00:00",
"file_format": "fastq",
"file_size": 516290095,
"href": "/sequence-files/IGVFFI7897TYMN/@@download/IGVFFI7897TYMN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/cd4891fa-83ca-4bef-8d00-f17ca22e2432/IGVFFI7897TYMN.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0022840/",
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230707_IGVF10_McGinnis/MULTI/FASTQ/MULTI_2_CMAS_IGVF10_R_S6_L005_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6476FJVC/",
"accession": "IGVFFI6476FJVC",
"aliases": [
"ansuman-satpathy:igvf_exp10_multi_10x2_NGS1_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T21:00:07.277572+00:00",
"file_format": "fastq",
"file_size": 1230298446,
"href": "/sequence-files/IGVFFI6476FJVC/@@download/IGVFFI6476FJVC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/09e4d2e6-96c8-4660-82b7-3e5e3a4dd8f3/IGVFFI6476FJVC.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0022840/",
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230707_IGVF10_McGinnis/MULTI/FASTQ/MULTI_2_CMAS_IGVF10_R_S6_L004_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2629AQFQ/",
"accession": "IGVFFI2629AQFQ",
"aliases": [
"ansuman-satpathy:igvf_exp10_multi_10x2_NGS1_i2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T21:00:27.589300+00:00",
"file_format": "fastq",
"file_size": 162645630,
"href": "/sequence-files/IGVFFI2629AQFQ/@@download/IGVFFI2629AQFQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/35c26631-e589-4b6f-8d7e-8fa4f4c9b26d/IGVFFI2629AQFQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0022840/",
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230707_IGVF10_McGinnis/MULTI/FASTQ/MULTI_2_CMAS_IGVF10_R_S6_L004_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5233TBNI/",
"accession": "IGVFFI5233TBNI",
"aliases": [
"ansuman-satpathy:igvf_exp10_multi_10x2_NGS2_r2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T21:00:45.179376+00:00",
"file_format": "fastq",
"file_size": 1161678269,
"href": "/sequence-files/IGVFFI5233TBNI/@@download/IGVFFI5233TBNI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/0efa3bce-0cb1-4aaf-bae2-0891d97197a5/IGVFFI5233TBNI.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0022840/",
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230707_IGVF10_McGinnis/MULTI/FASTQ/MULTI_2_CMAS_IGVF10_R_S6_L005_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6902ZMDQ/",
"accession": "IGVFFI6902ZMDQ",
"aliases": [
"ansuman-satpathy:igvf_exp10_multi_10x2_NGS1_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T21:00:20.066005+00:00",
"file_format": "fastq",
"file_size": 216096628,
"href": "/sequence-files/IGVFFI6902ZMDQ/@@download/IGVFFI6902ZMDQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/706d8407-ab6b-4126-9110-bd41115caf4b/IGVFFI6902ZMDQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0022840/",
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230707_IGVF10_McGinnis/MULTI/FASTQ/MULTI_2_CMAS_IGVF10_R_S6_L004_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6071USFB/",
"accession": "IGVFFI6071USFB",
"aliases": [
"ansuman-satpathy:igvf_exp10_multi_10x2_NGS2_i1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T21:00:57.509625+00:00",
"file_format": "fastq",
"file_size": 203241178,
"href": "/sequence-files/IGVFFI6071USFB/@@download/IGVFFI6071USFB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/8d947424-6e69-4546-8103-993767f067a6/IGVFFI6071USFB.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0022840/",
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230707_IGVF10_McGinnis/MULTI/FASTQ/MULTI_2_CMAS_IGVF10_R_S6_L005_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6206DFYP/",
"accession": "IGVFFI6206DFYP",
"aliases": [
"ansuman-satpathy:igvf_exp10_multi_10x2_NGS2_i2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T21:01:05.385896+00:00",
"file_format": "fastq",
"file_size": 154742620,
"href": "/sequence-files/IGVFFI6206DFYP/@@download/IGVFFI6206DFYP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/07/22/cd24d8a9-8d9a-404f-9d2d-92e97d6c6a3b/IGVFFI6206DFYP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0022840/",
"status": "released",
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230707_IGVF10_McGinnis/MULTI/FASTQ/MULTI_2_CMAS_IGVF10_R_S6_L005_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5181NANQ/",
"accession": "IGVFFI5181NANQ",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp10_multi_10x2_NGS1"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:21:57.832188+00:00",
"file_format": "yaml",
"file_size": 1336,
"href": "/configuration-files/IGVFFI5181NANQ/@@download/IGVFFI5181NANQ.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/954882dd-45af-4b81-abbe-a1c8e1efcd14/IGVFFI5181NANQ.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp10_multi_10x2_NGS1_multi_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9144IRYG/",
"accession": "IGVFFI9144IRYG",
"aliases": [
"ansuman-satpathy:seqspec_igvf_exp10_multi_10x2_NGS2"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-18T02:22:01.271183+00:00",
"file_format": "yaml",
"file_size": 1336,
"href": "/configuration-files/IGVFFI9144IRYG/@@download/IGVFFI9144IRYG.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/18/bca2b156-a2a0-47e0-97f0-5e905133466a/IGVFFI9144IRYG.yaml.gz",
"status": "released",
"submitted_file_name": "/home/users/cmcginni/igvf_utils_out/seqspec/igvf_exp10_multi_10x2_NGS2_multi_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2018URDY/"
],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1013HCXI/",
"accession": "IGVFDS1013HCXI",
"aliases": [
"ansuman-satpathy:snATAC-seq_igvf10_10x2"
],
"preferred_assay_title": "10x multiome with MULTI-seq",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9139TBCB/",
"accession": "IGVFDS9139TBCB",
"aliases": [
"ansuman-satpathy:snRNA-seq_igvf10_10x2"
],
"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": "2025-03-07T01:13:48.626843+00:00",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM0539NUPM/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM0539NUPM",
"aliases": [
"ansuman-satpathy:multiplexed_sample_igvf10_10x2"
],
"classifications": [
"cell line",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"modality": "interference",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
},
{
"@id": "/sample-terms/EFO_0002067/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:K562"
],
"status": "released",
"summary": "K562",
"term_name": "K562"
},
{
"@id": "/sample-terms/EFO_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
},
{
"@id": "/sample-terms/NTR_0000753/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:TeloHAEC"
],
"status": "released",
"summary": "TeloHAEC",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "multiplexed sample: Jurkat cell line, male, Homo sapiens treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours; K562 cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB; ... and 8 more samples",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours",
"treatment_type": "chemical"
},
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours",
"treatment_type": "protein"
}
]
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_files_timestamp": "2024-07-22T20:59:54.557458+00:00",
"summary": "lipid-conjugated oligo sequencing for interference single-nucleus ATAC-seq (10x multiome with MULTI-seq), interference single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)",
"uuid": "c1a6fbba-9ea5-4e99-9501-d116481317ab"
}