{
"@context": "/terms/",
"@id": "/sequence-files/IGVFFI6421BIVI/",
"@type": [
"SequenceFile",
"File",
"Item"
],
"accession": "IGVFFI6421BIVI",
"aliases": [
"ansuman-satpathy:igvf_exp10_atac_10x1_NGS1_r1"
],
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {},
"award": {
"@id": "/awards/HG012076/",
"component": "mapping"
},
"content_md5sum": "e5d831bee1144d6a4fc17d4a9bc9b74c",
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-07-22T16:43:33.289823+00:00",
"externally_hosted": false,
"file_format": "fastq",
"file_set": {
"@id": "/measurement-sets/IGVFDS3910GBDQ/",
"accession": "IGVFDS3910GBDQ",
"file_set_type": "experimental data",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM4547BFMA/",
"accession": "IGVFSM4547BFMA",
"classifications": [
"cell line",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
},
{
"@id": "/sample-terms/EFO_0002067/",
"status": "released",
"term_name": "K562"
},
{
"@id": "/sample-terms/EFO_0002796/",
"status": "released",
"term_name": "Jurkat"
},
{
"@id": "/sample-terms/NTR_0000753/",
"status": "released",
"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_term_name": "phorbol 13-acetate 12-myristate"
},
{
"@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_term_name": "T-cell surface glycoprotein CD3 gamma chain"
}
]
}
],
"status": "released",
"summary": "interference single-nucleus ATAC-seq (10x multiome with MULTI-seq)"
},
"file_size": 17247848465,
"flowcell_id": "223JKJLT3",
"gene_list_for": [],
"href": "/sequence-files/IGVFFI6421BIVI/@@download/IGVFFI6421BIVI.fastq.gz",
"illumina_read_type": "R1",
"input_file_for": [
"/tabular-files/IGVFFI0627MDWY/"
],
"integrated_in": [],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"lane": 7,
"loci_list_for": [],
"maximum_read_length": 50,
"md5sum": "24e0699e1221037c71bf4d0a43ea1438",
"mean_read_length": 50,
"minimum_read_length": 50,
"quality_metrics": [],
"read_count": 597871724,
"read_names": [
"Read 1"
],
"release_timestamp": "2025-03-07T01:13:44.425927+00:00",
"s3_uri": "s3://igvf-files/2024/07/22/bbcc272e-854a-4b16-8bc2-b01ffe30007b/IGVFFI6421BIVI.fastq.gz",
"schema_version": "15",
"seqspecs": [
"/configuration-files/IGVFFI8451KNKW/"
],
"sequencing_kit": "NovaSeq X Series 10B Reagent Kit",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"sequencing_run": 1,
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_file_name": "/oak/stanford/projects/igvf/Projects/230707_IGVF10_McGinnis/ATAC/FASTQ/ATAC_1_S130_L007_R1_001.fastq.gz",
"summary": "R1 reads from sequencing run 1",
"upload_status": "validated",
"uuid": "bbcc272e-854a-4b16-8bc2-b01ffe30007b"
}