{
"@context": "/terms/",
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"File",
"Item"
],
"accession": "IGVFFI7411STSC",
"aliases": [
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],
"analysis_step_version": "/analysis-step-versions/699d6738-4033-4afc-b6f3-1d82a80e0b41/",
"assay_titles": [
"10x multiome with MULTI-seq"
],
"assembly": "GRCh38",
"audit": {},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"barcode_map_for": [],
"checkfiles_version": "v14",
"content_md5sum": "cf11d640a4b43888a2aba2548b72522f",
"content_type": "peaks",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:06:13.955869+00:00",
"derived_from": [
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],
"file_format": "bed",
"file_format_specifications": [
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],
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"accession": "IGVFDS2018URDY",
"file_set_type": "intermediate analysis",
"samples": [
{
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"accession": "IGVFSM4547BFMA",
"classifications": [
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"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"
},
{
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"status": "released",
"term_name": "K562"
},
{
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"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": [
{
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"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"
}
]
},
{
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"classifications": [
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],
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{
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"modality": "interference",
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"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
}
],
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{
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"status": "released",
"term_name": "THP-1"
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{
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},
{
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},
{
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"term_name": "TeloHAEC"
}
],
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"taxa": "Homo sapiens",
"treatments": [
{
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"purpose": "stimulation",
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},
{
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"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"
}
]
}
],
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"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix"
},
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"href": "/tabular-files/IGVFFI7411STSC/@@download/IGVFFI7411STSC.bed.gz",
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"lab": {
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"title": "Ansuman Satpathy, Stanford"
},
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"quality_metrics": [],
"release_timestamp": "2025-03-07T06:04:55.808557+00:00",
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"schema_version": "13",
"status": "released",
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"title": "Christopher Mcginnis"
},
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf10/e10l2_peaks.bed",
"summary": "GRCh38 peaks",
"upload_status": "validation exempted",
"uuid": "79774340-e7e6-45b9-851f-6104376fb0fd",
"validation_error_detail": "{\"md5sum\": \"original md5sum cf11d640a4b43888a2aba2548b72522f does not match newly calculated md5sum 2dddd59888acec9f879c65812c93b776.\", \"validate_files\": \"Error [file=/home/ubuntu/igvf-files/2025/01/28/79774340-e7e6-45b9-851f-6104376fb0fd/IGVFFI7411STSC.bed.gz, line=190232]: chrom KI270728.1 not found [KI270728.1\\t232271\\t233171]\\nAborting ... found error.\"}",
"workflow": {
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"name": "Satpathy Cell Ranger",
"uniform_pipeline": false
}
}