IGVFFI5988KABT

released
validation exempted
1{
2    "@context": "/terms/",
3    "@id": "/tabular-files/IGVFFI5988KABT/",
4    "@type": [
5        "TabularFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI5988KABT",
10    "aliases": [
11        "ansuman-satpathy:igvf18_peaks_10x2"
12    ],
13    "analysis_step_version": "/analysis-step-versions/699d6738-4033-4afc-b6f3-1d82a80e0b41/",
14    "assay_titles": [
15        "10x multiome with MULTI-seq"
16    ],
17    "assembly": "GRCh38",
18    "audit": {},
19    "award": {
20        "@id": "/awards/HG011972/",
21        "component": "functional characterization"
22    },
23    "barcode_map_for": [],
24    "checkfiles_version": "v14",
25    "content_md5sum": "c499d6d93ee6d26d30377a81f829ce6f",
26    "content_type": "peaks",
27    "controlled_access": false,
28    "creation_timestamp": "2025-01-28T06:36:42.900320+00:00",
29    "derived_from": [
30        "/tabular-files/IGVFFI7984FWDE/"
31    ],
32    "file_format": "bed",
33    "file_format_specifications": [
34        {
35            "@id": "/documents/07404908-2ed4-4286-8345-97e0fc205b36/",
36            "description": "10X Genomics Peaks Bedfile"
37        }
38    ],
39    "file_format_type": "bed3",
40    "file_set": {
41        "@id": "/analysis-sets/IGVFDS7252MTQC/",
42        "@type": [
43            "AnalysisSet",
44            "FileSet",
45            "Item"
46        ],
47        "accession": "IGVFDS7252MTQC",
48        "controlled_access": false,
49        "data_use_limitation_summaries": [
50            "No limitations"
51        ],
52        "file_set_type": "intermediate analysis",
53        "samples": [
54            {
55                "@id": "/multiplexed-samples/IGVFSM9642EHZY/",
56                "@type": [
57                    "MultiplexedSample",
58                    "Sample",
59                    "Item"
60                ],
61                "accession": "IGVFSM9642EHZY",
62                "classifications": [
63                    "cell line",
64                    "differentiated cell specimen",
65                    "multiplexed sample"
66                ],
67                "disease_terms": [],
68                "modifications": [],
69                "sample_terms": [
70                    {
71                        "@id": "/sample-terms/EFO_0001196/",
72                        "status": "released",
73                        "term_name": "IMR-90"
74                    },
75                    {
76                        "@id": "/sample-terms/EFO_0001203/",
77                        "status": "released",
78                        "term_name": "MCF-7"
79                    },
80                    {
81                        "@id": "/sample-terms/EFO_0002824/",
82                        "status": "released",
83                        "term_name": "HCT116"
84                    },
85                    {
86                        "@id": "/sample-terms/EFO_0003072/",
87                        "status": "released",
88                        "term_name": "SK-N-SH"
89                    },
90                    {
91                        "@id": "/sample-terms/EFO_0022838/",
92                        "status": "released",
93                        "term_name": "HUDEP-2"
94                    },
95                    {
96                        "@id": "/sample-terms/NTR_0000753/",
97                        "status": "released",
98                        "term_name": "TeloHAEC"
99                    }
100                ],
101                "status": "released",
102                "summary": "multiplexed sample: Homo sapiens (female) IMR-90 cell line; Homo sapiens (female) MCF-7 cell line; ... and 17 more samples",
103                "taxa": "Homo sapiens",
104                "treatments": [
105                    {
106                        "@id": "/treatments/ff03c6ff-c1f5-4b47-bd9d-62f22d5794c5/",
107                        "purpose": "perturbation",
108                        "status": "in progress",
109                        "summary": "Treatment of 3 μM Yoda1 for 4 hours",
110                        "treatment_term_name": "Yoda1"
111                    }
112                ]
113            }
114        ],
115        "status": "released",
116        "summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)"
117    },
118    "file_size": 1680971,
119    "gene_list_for": [],
120    "href": "/tabular-files/IGVFFI5988KABT/@@download/IGVFFI5988KABT.bed.gz",
121    "input_file_for": [],
122    "integrated_in": [],
123    "lab": {
124        "@id": "/labs/ansuman-satpathy/",
125        "title": "Ansuman Satpathy, Stanford"
126    },
127    "loci_list_for": [],
128    "md5sum": "6e6ced2ef8d4b71eedd05f3f4fc5612f",
129    "primer_design_for": [],
130    "quality_metrics": [],
131    "release_timestamp": "2025-03-07T06:05:35.362478+00:00",
132    "s3_uri": "s3://igvf-files/2025/01/28/b7af376b-6ae6-4545-935e-4e28a25e1ffb/IGVFFI5988KABT.bed.gz",
133    "schema_version": "15",
134    "status": "released",
135    "submitted_by": {
136        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
137        "title": "Christopher Mcginnis"
138    },
139    "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf18/e18l2_peaks.bed",
140    "summary": "GRCh38 peaks",
141    "upload_status": "validation exempted",
142    "uuid": "b7af376b-6ae6-4545-935e-4e28a25e1ffb",
143    "validation_error_detail": "{\"md5sum\": \"original md5sum c499d6d93ee6d26d30377a81f829ce6f does not match newly calculated md5sum 6e6ced2ef8d4b71eedd05f3f4fc5612f.\", \"validate_files\": \"Error [file=/home/ubuntu/igvf-files/2025/01/28/b7af376b-6ae6-4545-935e-4e28a25e1ffb/IGVFFI5988KABT.bed.gz, line=202909]: chrom KI270728.1 not found [KI270728.1\\t232286\\t233180]\\nAborting ... found error.\"}",
144    "workflow": {
145        "@id": "/workflows/IGVFWF1453HVEC/",
146        "name": "Satpathy Cell Ranger",
147        "uniform_pipeline": false
148    }
149}