This tab provides a complete list of all metadata files submitted by the atlas.

Synapse ID	Category	Num Records	Percent Complete Metadata
syn66366532	10XGenomicsXeniumISSExperiment	32	90.00%
syn39283683	Biospecimen	288	20.64%
syn66312808	Biospecimen	35	29.93%
syn51718142	BulkMethylation-seqLevel1	80	73.33%
syn51934273	BulkMethylation-seqLevel2	51	40.62%
syn39282161	BulkRNA-seqLevel1	348	26.23%
syn60979705	BulkRNA-seqLevel1	72	28.57%
syn60986363	BulkRNA-seqLevel3	36	81.25%
syn53361674	BulkWESLevel1	506	46.61%
syn53351688	BulkWESLevel1	126	50.00%
syn53366794	BulkWESLevel2	108	20.83%
syn53359881	BulkWESLevel2	51	20.83%
syn61516871	CDSSequencingTemplate	23	30.77%
syn61000678	CDSSequencingTemplate	46	63.64%
syn39283850	Demographics	40	23.09%
syn39284405	Diagnosis	16	6.81%
syn39284881	Exposure	16	6.67%
syn39285152	FamilyHistory	16	25.00%
syn39285191	FollowUp	16	3.57%
syn51526303	HI-C-seqLevel1	66	100.00%
syn51702921	HI-C-seqLevel2	34	100.00%
syn58828438	HI-C-seqLevel3	2	60.00%
syn66330073	ImagingLevel1	32	91.67%
syn53335738	ImagingLevel1	16	75.00%
syn53339259	ImagingLevel2	71	77.78%
syn53335787	ImagingLevel3Segmentation	1598	75.00%
syn53408884	ImagingLevel4	70	71.43%
syn53711322	MassSpectrometryLevel1	494	90.32%
syn53711588	MassSpectrometryLevel1	214	96.77%
syn51703772	MassSpectrometryLevel1	479	100.00%
syn51732852	MassSpectrometryLevel3	28	100.00%
syn51732873	MassSpectrometryLevel4	28	100.00%
syn39283342	ScATAC-seqLevel1	640	74.03%
syn52177151	ScATAC-seqLevel2	17	33.61%
syn61064183	ScATAC-seqLevel3	80	13.64%
syn39283525	ScRNA-seqLevel1	384	78.98%
syn39285399	ScRNA-seqLevel2	128	91.57%
syn39285463	ScRNA-seqLevel3	192	83.33%
syn39285223	Therapy	16	9.52%

This tab provides a complete list of all validation errors detected by the dashboard.

10XGenomicsXeniumISSExperiment is not yet supported by the Dashboard. Please notify Ethan to update the code!
CDSSequencingTemplate is not yet supported by the Dashboard. Please notify Ethan to update the code!

Validation Passed.

In folder: codex_level_4/A001-C-002, file name: A001-C-002__(Reg2)_reg002_compensated.csv contains unsupported characters.
In folder: codex_level_4/A015-C-202, file name: A015-C-202_(Reg1)_reg001_compensated.csv contains unsupported characters.
In folder: codex_level_4/A001-C-023, file name: A001-C-023_(Reg1)_compensated.csv contains unsupported characters.
In folder: codex_level_4/A002-C-024, file name: A002-C-024_(Reg2)_reg002_compensated.csv contains unsupported characters.
In folder: codex_level_4/A001-C-124, file name: A001-C-124_(Reg1)_reg001_compensated.csv contains unsupported characters.
In folder: lipidomics/batch-1/mode-2, file name: F-NL-CEC_(F-Asc-001).mzML contains unsupported characters.
In folder: lipidomics/batch-1/mode-1, file name: F-NL-CEC_(F-Asc-001).mzML contains unsupported characters.
In folder: lipidomics/batch-1/mode-1, file name: F-NL-TR_(F-Trans-001).mzML contains unsupported characters.
In folder: lipidomics/batch-1/mode-2, file name: F-NL-TR_(F-Trans-001).mzML contains unsupported characters.
In folder: metabolomics/Batch 1/pHILIC, file name: F-NL-CEC_(F-Asc-001).raw contains unsupported characters.
In folder: metabolomics/Batch 1/pRPLC, file name: F-NL-CEC_(F-Asc-001).raw contains unsupported characters.
In folder: metabolomics/Batch 1/nRPLC, file name: F-NL-CEC_(F-Asc-001).raw contains unsupported characters.
In folder: metabolomics/Batch 1/nHILIC, file name: F-NL-CEC_(F-Asc-001).raw contains unsupported characters.
In folder: metabolomics/Batch 1/nRPLC, file name: F-NL-TR_(F-Trans-001).raw contains unsupported characters.
In folder: metabolomics/Batch 1/pRPLC, file name: F-NL-TR_(F-Trans-001).raw contains unsupported characters.
In folder: metabolomics/Batch 1/nHILIC, file name: F-NL-TR_(F-Trans-001).raw contains unsupported characters.
In folder: metabolomics/Batch 1/pHILIC, file name: F-NL-TR_(F-Trans-001).raw contains unsupported characters.
In folder: codex_level_4/A001-C-108, file name: Codex Analysis_A001-C-108.fcs contains unsupported characters.
In folder: codex_level_4/A001-C-104, file name: Codex Analysis_A001-C-104.fcs contains unsupported characters.

These plots are designed to visually summarize the data completeness of an HTAN atlas.

For example:

how much Tier 1 clinical data has the atlas provided?
for sequencing or imaging data, has the atlas provided Level 1-4 data?

Clinical Data Matrix: Tiers 1 and 2

ParticipantID	Demographics	Exposure	FamilyHistory	FollowUp	Diagnosis	Therapy
HTA10_01	1	1	1	1	1	1
HTA10_02	1	1	1	1	1	1
HTA10_03	1	1	1	1	1	1
HTA10_04	1	1	1	1	1	1
HTA10_05	1	1	1	1	1	1
HTA10_06	1	1	1	1	1	1
HTA10_07	1	1	1	1	1	1
HTA10_08	1	1	1	1	1	1
HTA10_09	1	1	1	1	1	1
HTA10_10	1	1	1	1	1	1
HTA10_11	1	1	1	1	1	1
HTA10_12	1	1	1	1	1	1
HTA10_13	1	1	1	1	1	1
HTA10_15	1	0	0	0	0	0
HTA10_16	1	0	0	0	0	0
HTA10_17	1	0	0	0	0	0
HTA10_18	1	1	1	1	1	1
HTA10_19	1	0	0	0	0	0
HTA10_20	1	0	0	0	0	0
HTA10_21	1	0	0	0	0	0
HTA10_22	1	1	1	1	1	1
HTA10_23	1	0	0	0	0	0
HTA10_24	1	0	0	0	0	0
HTA10_25	1	0	0	0	0	0
HTA10_26	1	0	0	0	0	0
HTA10_27	1	0	0	0	0	0
HTA10_28	1	0	0	0	0	0
HTA10_29	1	0	0	0	0	0
HTA10_30	1	0	0	0	0	0
HTA10_31	1	0	0	0	0	0
HTA10_32	1	0	0	0	0	0
HTA10_33	1	0	0	0	0	0
HTA10_34	1	0	0	0	0	0
HTA10_35	1	0	0	0	0	0
HTA10_36	1	0	0	0	0	0
HTA10_37	1	0	0	0	0	0
HTA10_38	1	0	0	0	0	0
HTA10_39	1	0	0	0	0	0
HTA10_40	1	0	0	0	0	0
HTA10_41	1	0	0	0	0	0

	Counts
Demographics	40
Exposure	15
FamilyHistory	15
FollowUp	15
Diagnosis	15
Therapy	15
MolecularTest	0
ClinicalDataTier2	0
SRRSClinicalDataTier2	0

Clinical Data Matrix: Tier 3

No data available.

ParticipantID	AcuteLym..	Neurobla..	BreastCa..	Colorect..	LungCanc..	Melanoma..	OvarianC..	Pancreat..	Prostate..	SarcomaT..
HTA10_01	0	0	0	0	0	0	0	0	0	0
HTA10_02	0	0	0	0	0	0	0	0	0	0
HTA10_03	0	0	0	0	0	0	0	0	0	0
HTA10_04	0	0	0	0	0	0	0	0	0	0
HTA10_05	0	0	0	0	0	0	0	0	0	0
HTA10_06	0	0	0	0	0	0	0	0	0	0
HTA10_07	0	0	0	0	0	0	0	0	0	0
HTA10_08	0	0	0	0	0	0	0	0	0	0
HTA10_09	0	0	0	0	0	0	0	0	0	0
HTA10_10	0	0	0	0	0	0	0	0	0	0
HTA10_11	0	0	0	0	0	0	0	0	0	0
HTA10_12	0	0	0	0	0	0	0	0	0	0
HTA10_13	0	0	0	0	0	0	0	0	0	0
HTA10_15	0	0	0	0	0	0	0	0	0	0
HTA10_16	0	0	0	0	0	0	0	0	0	0
HTA10_17	0	0	0	0	0	0	0	0	0	0
HTA10_18	0	0	0	0	0	0	0	0	0	0
HTA10_19	0	0	0	0	0	0	0	0	0	0
HTA10_20	0	0	0	0	0	0	0	0	0	0
HTA10_21	0	0	0	0	0	0	0	0	0	0
HTA10_22	0	0	0	0	0	0	0	0	0	0
HTA10_23	0	0	0	0	0	0	0	0	0	0
HTA10_24	0	0	0	0	0	0	0	0	0	0
HTA10_25	0	0	0	0	0	0	0	0	0	0
HTA10_26	0	0	0	0	0	0	0	0	0	0
HTA10_27	0	0	0	0	0	0	0	0	0	0
HTA10_28	0	0	0	0	0	0	0	0	0	0
HTA10_29	0	0	0	0	0	0	0	0	0	0
HTA10_30	0	0	0	0	0	0	0	0	0	0
HTA10_31	0	0	0	0	0	0	0	0	0	0
HTA10_32	0	0	0	0	0	0	0	0	0	0
HTA10_33	0	0	0	0	0	0	0	0	0	0
HTA10_34	0	0	0	0	0	0	0	0	0	0
HTA10_35	0	0	0	0	0	0	0	0	0	0
HTA10_36	0	0	0	0	0	0	0	0	0	0
HTA10_37	0	0	0	0	0	0	0	0	0	0
HTA10_38	0	0	0	0	0	0	0	0	0	0
HTA10_39	0	0	0	0	0	0	0	0	0	0
HTA10_40	0	0	0	0	0	0	0	0	0	0
HTA10_41	0	0	0	0	0	0	0	0	0	0

	Counts
AcuteLym..	0
Neurobla..	0
BreastCa..	0
Colorect..	0
LungCanc..	0
Melanoma..	0
OvarianC..	0
Pancreat..	0
Prostate..	0
SarcomaT..	0

Assay Matrix: Single Cell Data

BiospecimenID	ScRNA-seqLevel1	ScRNA-seqLevel2	ScRNA-seqLevel3	ScATAC-seqLevel1	ScATAC-seqLevel2	ScATAC-seqLevel3
HTA10_01_002	0	0	0	1	0	1
HTA10_01_007	1	1	1	1	0	1
HTA10_01_014	1	1	1	1	1	1
HTA10_01_023	1	1	1	1	0	1
HTA10_01_104	1	1	1	1	0	1
HTA10_01_108	1	1	1	1	1	1
HTA10_01_119	1	1	1	1	0	1
HTA10_01_123	0	0	0	1	1	1
HTA10_01_124	1	1	1	1	0	1
HTA10_01_202	1	1	1	1	0	1
HTA10_01_203	1	1	1	1	0	1
HTA10_01_207	1	1	1	1	0	1
HTA10_01_218	0	0	0	1	0	1
HTA10_01_223	1	1	1	1	0	1
HTA10_02_010	1	1	1	1	1	1
HTA10_02_016	1	1	1	1	0	1
HTA10_02_021	1	1	1	1	0	1
HTA10_02_024	1	1	1	1	1	1
HTA10_02_025	0	0	0	1	0	1
HTA10_02_106	1	1	1	1	0	1
HTA10_02_114	1	1	1	1	0	1
HTA10_02_116	1	1	1	1	0	1
HTA10_02_121	1	1	1	1	1	1
HTA10_02_201	1	1	1	1	0	0
HTA10_02_202	0	0	0	1	1	1
HTA10_02_203	1	1	1	1	0	0
HTA10_02_204	1	1	1	1	0	1
HTA10_02_205	1	1	1	1	1	1
HTA10_02_212	1	1	1	1	0	1
HTA10_03_001	1	1	1	1	0	0
HTA10_03_002	0	0	0	1	0	1
HTA10_03_008	1	1	1	1	0	1
HTA10_03_013	0	0	0	1	0	1
HTA10_03_040	1	1	1	1	0	1
HTA10_03_043	1	1	1	1	0	0
HTA10_03_052	1	1	1	1	0	0
HTA10_03_054	1	1	1	1	0	0
HTA10_03_101	1	1	1	1	0	0
HTA10_03_108	1	1	1	1	0	0
HTA10_03_111	1	1	1	1	0	0
HTA10_03_114	1	1	1	1	0	0
HTA10_03_201	1	1	1	1	1	0
HTA10_04_001	1	1	1	1	0	1
HTA10_04_002	1	1	1	1	0	1
HTA10_04_005	1	1	1	1	0	1
HTA10_04_006	1	1	1	1	0	1
HTA10_04_008	1	1	1	1	0	1
HTA10_04_010	1	1	1	1	1	1
HTA10_04_102	0	0	0	1	0	1
HTA10_04_104	1	1	1	1	0	1
HTA10_04_106	1	1	1	1	0	1
HTA10_04_109	1	1	1	1	1	1
HTA10_04_202	1	1	1	1	0	1
HTA10_04_203	1	1	1	1	0	1
HTA10_04_204	1	1	1	1	0	1
HTA10_04_206	0	0	0	1	0	1
HTA10_04_208	1	1	1	1	0	1
HTA10_05_007	1	1	1	1	1	1
HTA10_05_034	1	1	1	1	1	1
HTA10_05_072	1	1	1	1	1	1
HTA10_05_091	1	1	1	1	1	1
HTA10_08_008	1	1	1	1	0	0
HTA10_08_015	1	1	1	1	0	0
HTA10_09_111	1	1	1	1	0	1
HTA10_10_018	1	1	1	1	1	0
HTA10_10_023	1	1	1	1	0	0
HTA10_11_112	1	1	1	1	0	1
HTA10_12_113	1	1	1	1	0	1
HTA10_13_114	0	0	0	1	0	1
HTA10_18_013	1	1	1	1	0	1
HTA10_18_020	1	1	1	1	0	1
HTA10_22_002	1	1	1	1	1	1

	Counts
ScRNA-seqLevel1	62
ScRNA-seqLevel2	62
ScRNA-seqLevel3	62
ScRNA-seqLevel4	0
ScATAC-seqLevel1	72
ScATAC-seqLevel2	17
ScATAC-seqLevel3	57
ScATAC-seqLevel4	0

Assay Matrix: Bulk Data

BiospecimenID	BulkRNA-seqLevel1	BulkRNA-seqLevel3	BulkWESLevel1	BulkWESLevel2	BulkMethylation-seqLevel1	BulkMethylation-seqLevel2	HI-C-seqLevel1	HI-C-seqLevel2	HI-C-seqLevel3
HTA10_01_004	1	0	1	1	1	1	0	0	0
HTA10_01_005	1	0	1	1	1	1	0	0	0
HTA10_01_007	1	1	1	1	1	1	1	1	1
HTA10_01_008	0	0	0	0	0	0	1	1	1
HTA10_01_011	1	1	0	0	0	0	1	1	1
HTA10_01_013	1	1	0	0	0	0	1	1	1
HTA10_01_019	1	1	0	0	0	0	1	1	1
HTA10_01_021	1	0	1	1	1	1	0	0	0
HTA10_01_023	0	0	0	0	0	0	1	1	1
HTA10_01_024	0	0	0	0	0	0	1	1	1
HTA10_01_102	1	0	1	1	0	0	0	0	0
HTA10_01_107	1	0	1	1	0	0	0	0	0
HTA10_01_113	0	0	0	0	1	1	0	0	0
HTA10_01_122	1	0	1	1	0	0	0	0	0
HTA10_01_124	1	0	1	1	0	0	0	0	0
HTA10_01_206	0	0	0	0	1	1	0	0	0
HTA10_01_210	1	0	1	1	0	0	0	0	0
HTA10_01_214	1	0	1	1	0	0	0	0	0
HTA10_01_219	1	0	1	1	0	0	0	0	0
HTA10_01_222	1	0	1	1	0	0	0	0	0
HTA10_01_900	0	0	1	1	1	1	0	0	0
HTA10_02_001	1	1	0	0	0	0	1	1	1
HTA10_02_002	1	1	0	0	0	0	1	1	1
HTA10_02_006	1	1	0	0	0	0	1	1	1
HTA10_02_010	1	1	1	1	1	1	1	1	1
HTA10_02_012	0	0	0	0	1	1	1	1	1
HTA10_02_013	1	1	0	0	0	0	1	1	1
HTA10_02_016	1	0	1	1	0	0	0	0	0
HTA10_02_019	1	0	1	1	0	0	0	0	0
HTA10_02_020	1	0	1	1	0	0	0	0	0
HTA10_02_021	1	0	1	1	0	0	0	0	0
HTA10_02_022	1	0	1	1	0	0	0	0	0
HTA10_02_023	1	0	1	1	0	0	0	0	0
HTA10_02_024	1	0	1	1	0	0	0	0	0
HTA10_02_025	1	0	1	1	0	0	0	0	0
HTA10_02_102	1	0	1	1	0	0	0	0	0
HTA10_02_103	1	0	1	1	0	0	0	0	0
HTA10_02_107	1	0	1	1	0	0	0	0	0
HTA10_02_111	0	0	0	0	1	1	0	0	0
HTA10_02_116	1	0	1	1	1	1	0	0	0
HTA10_02_121	1	0	1	1	1	1	0	0	0
HTA10_02_122	1	1	1	1	0	0	1	1	1
HTA10_02_123	1	0	1	1	0	0	0	0	0
HTA10_02_201	1	0	1	1	0	0	0	0	0
HTA10_02_202	1	0	1	1	0	0	0	0	0
HTA10_02_203	1	0	1	1	0	0	0	0	0
HTA10_02_204	1	0	1	1	1	1	0	0	0
HTA10_02_207	1	0	1	1	0	0	0	0	0
HTA10_02_209	1	0	1	1	0	0	0	0	0
HTA10_02_211	1	0	1	1	0	0	0	0	0
HTA10_02_212	1	1	1	1	1	1	1	1	1
HTA10_02_213	1	0	1	1	0	0	0	0	0
HTA10_02_900	0	0	1	1	1	1	0	0	0
HTA10_03_001	1	0	1	1	1	1	0	0	0
HTA10_03_004	0	0	0	0	0	0	1	1	1
HTA10_03_012	1	1	0	0	0	0	1	1	1
HTA10_03_037	0	0	0	0	1	1	0	0	0
HTA10_03_038	0	0	0	0	1	1	1	1	1
HTA10_03_040	1	1	0	0	0	0	1	1	1
HTA10_03_041	1	1	0	0	0	0	1	1	1
HTA10_03_044	0	0	0	0	1	1	0	0	0
HTA10_03_045	0	0	0	0	0	0	1	1	1
HTA10_03_046	1	1	0	0	0	0	1	1	1
HTA10_03_052	1	0	1	1	1	1	0	0	0
HTA10_03_053	1	1	0	0	0	0	1	1	1
HTA10_03_054	1	1	0	0	0	0	1	1	1
HTA10_03_055	1	0	1	1	0	0	0	0	0
HTA10_03_114	1	0	1	1	0	0	0	0	0
HTA10_03_115	0	0	0	0	1	1	0	0	0
HTA10_03_201	1	0	1	1	0	0	0	0	0
HTA10_03_202	0	0	0	0	1	1	0	0	0
HTA10_03_900	0	0	1	1	1	1	0	0	0
HTA10_04_001	1	0	1	1	0	0	0	0	0
HTA10_04_002	1	0	1	1	1	1	0	0	0
HTA10_04_004	1	1	0	0	0	0	1	1	1
HTA10_04_006	0	0	0	0	0	0	1	1	1
HTA10_04_008	1	0	1	1	1	1	0	0	0
HTA10_04_010	1	1	1	1	0	0	1	1	1
HTA10_04_102	1	0	1	1	0	0	0	0	0
HTA10_04_109	1	0	1	1	0	0	0	0	0
HTA10_04_203	0	0	0	0	1	1	0	0	0
HTA10_04_206	1	0	1	1	0	0	0	0	0
HTA10_04_900	0	0	1	1	1	1	0	0	0
HTA10_05_002	1	0	1	1	0	0	0	0	0
HTA10_05_004	1	0	1	1	0	0	0	0	0
HTA10_05_006	0	0	1	1	0	0	0	0	0
HTA10_05_007	1	0	1	1	1	1	0	0	0
HTA10_05_008	1	0	1	1	0	0	0	0	0
HTA10_05_009	1	0	1	1	0	0	0	0	0
HTA10_05_011	0	0	1	1	0	0	0	0	0
HTA10_05_020	0	0	1	1	0	0	0	0	0
HTA10_05_025	1	0	1	1	0	0	0	0	0
HTA10_05_026	0	0	1	1	0	0	0	0	0
HTA10_05_027	1	0	1	1	0	0	0	0	0
HTA10_05_031	0	0	1	1	0	0	0	0	0
HTA10_05_032	0	0	1	1	0	0	0	0	0
HTA10_05_034	0	0	0	0	1	1	0	0	0
HTA10_05_037	1	0	1	1	0	0	0	0	0
HTA10_05_038	1	0	1	1	0	0	0	0	0
HTA10_05_039	1	0	1	1	0	0	0	0	0
HTA10_05_040	1	0	1	1	0	0	0	0	0
HTA10_05_046	0	0	1	1	0	0	0	0	0
HTA10_05_053	1	0	1	1	0	0	0	0	0
HTA10_05_056	0	0	1	1	0	0	0	0	0
HTA10_05_057	0	0	1	1	0	0	0	0	0
HTA10_05_061	1	0	1	1	0	0	0	0	0
HTA10_05_063	1	0	1	1	0	0	0	0	0
HTA10_05_065	1	0	1	1	0	0	0	0	0
HTA10_05_072	1	0	1	1	0	0	0	0	0
HTA10_05_073	1	0	1	1	0	0	0	0	0
HTA10_05_074	0	0	1	1	0	0	0	0	0
HTA10_05_076	1	0	1	1	0	0	0	0	0
HTA10_05_080	1	0	1	1	0	0	0	0	0
HTA10_05_084	0	0	1	1	0	0	0	0	0
HTA10_05_088	1	0	1	1	1	1	0	0	0
HTA10_05_092	1	0	1	1	0	0	0	0	0
HTA10_05_095	1	0	1	1	0	0	0	0	0
HTA10_05_098	1	0	1	1	0	0	0	0	0
HTA10_05_101	0	0	1	1	0	0	0	0	0
HTA10_05_102	1	0	1	1	0	0	0	0	0
HTA10_05_104	1	0	0	0	0	0	0	0	0
HTA10_05_105	1	0	1	1	0	0	0	0	0
HTA10_05_106	1	0	0	0	0	0	0	0	0
HTA10_05_107	1	0	1	1	0	0	0	0	0
HTA10_05_108	1	0	1	1	0	0	0	0	0
HTA10_05_117	0	0	1	1	0	0	0	0	0
HTA10_05_118	0	0	1	1	0	0	0	0	0
HTA10_05_900	0	0	1	1	1	1	0	0	0
HTA10_06_002	1	0	1	1	0	0	0	0	0
HTA10_06_003	0	0	1	1	0	0	0	0	0
HTA10_06_004	1	0	1	1	0	0	0	0	0
HTA10_06_005	1	0	1	1	0	0	0	0	0
HTA10_06_006	1	0	1	1	0	0	0	0	0
HTA10_06_009	0	0	1	1	0	0	0	0	0
HTA10_06_013	1	0	1	1	0	0	0	0	0
HTA10_06_014	1	0	1	1	0	0	0	0	0
HTA10_06_024	1	0	1	1	0	0	0	0	0
HTA10_06_025	1	0	1	1	0	0	0	0	0
HTA10_06_031	0	0	1	1	0	0	0	0	0
HTA10_06_032	0	0	1	1	0	0	0	0	0
HTA10_06_034	0	0	1	1	0	0	0	0	0
HTA10_06_038	0	0	1	1	0	0	0	0	0
HTA10_06_039	1	0	1	1	0	0	0	0	0
HTA10_06_043	1	0	1	1	0	0	0	0	0
HTA10_06_044	1	0	1	1	0	0	0	0	0
HTA10_06_045	1	0	1	1	0	0	0	0	0
HTA10_06_049	1	0	1	1	0	0	0	0	0
HTA10_06_051	1	0	1	1	0	0	0	0	0
HTA10_06_055	1	0	1	1	0	0	0	0	0
HTA10_06_061	1	0	1	1	0	0	0	0	0
HTA10_06_062	1	0	1	1	0	0	0	0	0
HTA10_06_063	0	0	1	1	0	0	0	0	0
HTA10_06_064	0	0	1	1	0	0	0	0	0
HTA10_06_065	1	0	1	1	0	0	0	0	0
HTA10_06_069	0	0	1	1	0	0	0	0	0
HTA10_06_073	0	0	1	1	0	0	0	0	0
HTA10_06_079	1	0	1	1	0	0	0	0	0
HTA10_06_104	0	0	1	1	0	0	0	0	0
HTA10_06_105	1	0	1	1	0	0	0	0	0
HTA10_06_108	1	0	1	1	0	0	0	0	0
HTA10_06_109	1	0	1	1	0	0	0	0	0
HTA10_06_110	1	0	1	1	0	0	0	0	0
HTA10_06_124	0	0	1	1	0	0	0	0	0
HTA10_06_126	0	0	1	1	0	0	0	0	0
HTA10_06_900	0	0	1	1	0	0	0	0	0
HTA10_07_001	1	0	0	0	0	0	0	0	0
HTA10_07_006	1	0	0	0	0	0	0	0	0
HTA10_07_101	1	0	0	0	0	0	0	0	0
HTA10_07_201	1	0	0	0	0	0	0	0	0
HTA10_07_301	1	0	0	0	0	0	0	0	0
HTA10_07_401	1	0	0	0	0	0	0	0	0
HTA10_07_406	1	0	0	0	0	0	0	0	0
HTA10_07_501	1	0	0	0	0	0	0	0	0
HTA10_17_001	0	0	0	0	1	1	0	0	0
HTA10_17_003	0	0	0	0	1	1	0	0	0
HTA10_19_002	0	0	0	0	1	1	0	0	0
HTA10_20_002	0	0	0	0	1	1	0	0	0
HTA10_20_018	0	0	0	0	1	1	0	0	0
HTA10_20_019	0	0	0	0	1	1	0	0	0
HTA10_20_020	0	0	0	0	1	1	0	0	0
HTA10_20_021	0	0	0	0	1	1	0	0	0
HTA10_20_022	0	0	0	0	1	1	0	0	0
HTA10_20_023	0	0	0	0	1	1	0	0	0
HTA10_20_024	0	0	0	0	1	1	0	0	0
HTA10_21_016	0	0	0	0	1	1	0	0	0
HTA10_21_018	0	0	0	0	1	1	0	0	0
HTA10_23_012	0	0	0	0	1	1	0	0	0
HTA10_23_111	0	0	0	0	1	1	0	0	0
HTA10_23_211	0	0	0	0	1	1	0	0	0
HTA10_24_001	0	0	0	0	1	1	0	0	0
HTA10_25_001	0	0	0	0	1	1	0	0	0
HTA10_26_001	0	0	0	0	1	1	0	0	0
HTA10_27_001	0	0	0	0	1	1	0	0	0
HTA10_28_001	1	1	0	0	0	0	1	1	1
HTA10_29_001	1	1	0	0	0	0	1	1	1
HTA10_30_001	1	1	0	0	0	0	1	1	1
HTA10_31_001	0	0	0	0	0	0	1	1	1
HTA10_32_001	1	1	0	0	0	0	1	1	1
HTA10_33_001	1	1	0	0	0	0	1	1	1
HTA10_34_00402	1	1	0	0	0	0	0	0	0
HTA10_34_00403	1	1	0	0	0	0	0	0	0
HTA10_34_00802	1	1	0	0	0	0	0	0	0
HTA10_34_00803	1	1	0	0	0	0	0	0	0
HTA10_34_10302	1	1	0	0	0	0	0	0	0
HTA10_34_10303	1	1	0	0	0	0	0	0	0

	Counts
BulkRNA-seqLevel1	134
BulkRNA-seqLevel2	0
BulkRNA-seqLevel3	30
BulkRNA-seqLevel4	0
BulkWESLevel1	132
BulkWESLevel2	132
BulkWESLevel3	0
BulkWESLevel4	0
BulkMethylation-seqLevel1	51
BulkMethylation-seqLevel2	51
BulkMethylation-seqLevel3	0
BulkMethylation-seqLevel4	0
HI-C-seqLevel1	33
HI-C-seqLevel2	33
HI-C-seqLevel3	33
HI-C-seqLevel4	0

Assay Matrix: Core Imaging

BiospecimenID	ImagingLevel1	ImagingLevel2	ImagingLevel3Segmentation	ImagingLevel4
HTA10_01_002	1	1	1	1
HTA10_01_007	1	1	1	1
HTA10_01_023	1	1	1	1
HTA10_01_104	0	1	1	1
HTA10_01_108	0	1	1	1
HTA10_01_119	1	1	1	1
HTA10_01_124	1	1	1	1
HTA10_01_207	0	1	1	1
HTA10_02_016	0	1	1	1
HTA10_02_021	0	1	1	1
HTA10_02_024	1	1	1	1
HTA10_02_025	0	1	1	1
HTA10_02_106	0	1	1	1
HTA10_02_203	1	1	1	1
HTA10_02_204	0	1	1	1
HTA10_02_205	1	1	1	1
HTA10_02_211	0	1	1	1
HTA10_02_212	0	1	1	1
HTA10_03_002	1	1	1	1
HTA10_03_114	0	1	1	1
HTA10_04_005	1	1	1	1
HTA10_04_010	0	1	1	1
HTA10_04_202	1	1	1	1
HTA10_04_204	0	1	1	1
HTA10_04_206	0	1	1	1
HTA10_04_207	0	1	1	1
HTA10_04_208	0	1	1	1
HTA10_05_072	1	1	1	1
HTA10_06_024	0	1	1	1
HTA10_06_025	0	1	1	1
HTA10_06_043	0	1	1	1
HTA10_06_044	0	1	1	1
HTA10_06_051	0	1	1	1
HTA10_06_055	0	1	1	1
HTA10_06_061	0	1	1	1
HTA10_06_062	0	1	1	1
HTA10_06_105	0	1	1	1
HTA10_07_101	1	1	1	1
HTA10_07_201	0	1	1	1
HTA10_07_301	1	1	1	1
HTA10_07_401	1	1	1	1
HTA10_11_112	1	1	1	1
HTA10_15_058	0	1	1	1
HTA10_15_059	0	1	1	1
HTA10_16_112	0	1	1	1
HTA10_16_113	0	1	1	1
HTA10_16_115	0	1	1	1
HTA10_16_116	0	1	1	1
HTA10_18_014	0	1	1	1
HTA10_18_021	0	1	1	1
HTA10_20_045	0	1	1	1
HTA10_23_212	0	1	1	1
HTA10_23_213	0	1	1	1
HTA10_29_001	0	1	1	1
HTA10_30_001	0	1	1	1
HTA10_33_001	0	1	1	1
HTA10_34_052	0	1	1	1
HTA10_35_008	0	1	1	1
HTA10_36_002	0	1	1	1
HTA10_37_005	0	1	1	1
HTA10_37_006	0	1	1	1
HTA10_38_004	0	1	1	1
HTA10_38_008	0	1	1	1
HTA10_38_404	0	1	1	1
HTA10_38_408	0	1	1	1
HTA10_38_504	0	1	1	1
HTA10_39_002	0	1	1	1
HTA10_40_101	0	1	1	1
HTA10_41_00801	1	0	0	0
HTA10_41_00802	1	0	0	0
HTA10_41_00803	1	0	0	0
HTA10_41_00804	1	0	0	0
HTA10_41_00805	1	0	0	0
HTA10_41_00806	1	0	0	0
HTA10_41_00807	1	0	0	0
HTA10_41_00808	1	0	0	0
HTA10_41_00809	1	0	0	0
HTA10_41_00810	1	0	0	0
HTA10_41_00811	1	0	0	0
HTA10_41_00812	1	0	0	0
HTA10_41_00813	1	0	0	0
HTA10_41_00814	1	0	0	0
HTA10_41_00815	1	0	0	0
HTA10_41_00816	1	0	0	0
HTA10_41_00817	1	0	0	0
HTA10_41_00818	1	0	0	0
HTA10_41_00819	1	0	0	0
HTA10_41_00820	1	0	0	0
HTA10_41_00821	1	0	0	0
HTA10_41_00822	1	0	0	0
HTA10_41_00823	1	0	0	0
HTA10_41_00824	1	0	0	0
HTA10_41_00825	1	0	0	0
HTA10_41_00826	1	0	0	0
HTA10_41_00827	1	0	0	0
HTA10_41_00828	1	0	0	0
HTA10_41_00829	1	0	0	0
HTA10_41_00830	1	0	0	0
HTA10_41_00831	1	0	0	0
HTA10_41_00832	1	0	0	0

	Counts
ImagingLevel1	48
ImagingLevel2	68
ImagingLevel3Image	0
ImagingLevel3Channels	0
ImagingLevel3Segmentation	68
ImagingLevel4	68
SRRSImagingLevel2	0

Assay Matrix: Other

BiospecimenID	MassSpectrometryLevel1	MassSpectrometryLevel3	MassSpectrometryLevel4
HTA10_01_004	1	1	1
HTA10_01_005	1	1	1
HTA10_01_007	1	0	0
HTA10_01_021	1	1	1
HTA10_01_102	1	1	1
HTA10_01_107	1	1	1
HTA10_01_122	1	1	1
HTA10_01_124	1	1	1
HTA10_01_210	1	1	1
HTA10_01_214	1	1	1
HTA10_01_219	1	1	1
HTA10_01_222	1	1	1
HTA10_02_010	1	1	1
HTA10_02_016	1	1	1
HTA10_02_019	1	1	1
HTA10_02_021	1	1	1
HTA10_02_023	1	1	1
HTA10_02_024	1	1	1
HTA10_02_025	1	1	1
HTA10_02_103	1	1	1
HTA10_02_107	1	1	1
HTA10_02_116	1	1	1
HTA10_02_121	1	1	1
HTA10_02_122	1	1	1
HTA10_02_123	1	1	1
HTA10_02_201	1	1	1
HTA10_02_202	1	1	1
HTA10_02_203	1	1	1
HTA10_02_204	1	1	1
HTA10_02_207	1	1	1
HTA10_02_209	1	1	1
HTA10_02_211	1	1	1
HTA10_02_212	1	1	1
HTA10_02_213	1	1	1
HTA10_03_001	1	1	1
HTA10_03_052	1	1	1
HTA10_03_055	1	1	1
HTA10_03_114	1	1	1
HTA10_03_201	1	1	1
HTA10_04_001	1	1	1
HTA10_04_002	1	1	1
HTA10_04_008	1	1	1
HTA10_04_010	1	1	1
HTA10_04_102	1	1	1
HTA10_04_109	1	1	1
HTA10_04_206	1	1	1
HTA10_05_002	1	1	1
HTA10_05_004	1	1	1
HTA10_05_007	1	1	1
HTA10_05_008	1	1	1
HTA10_05_009	1	0	0
HTA10_05_025	1	1	1
HTA10_05_027	1	1	1
HTA10_05_037	1	1	1
HTA10_05_038	1	1	1
HTA10_05_039	1	1	1
HTA10_05_040	1	1	1
HTA10_05_046	1	1	1
HTA10_05_053	1	1	1
HTA10_05_061	1	1	1
HTA10_05_063	1	1	1
HTA10_05_065	1	1	1
HTA10_05_072	1	1	1
HTA10_05_073	1	1	1
HTA10_05_074	1	1	1
HTA10_05_076	1	1	1
HTA10_05_088	1	1	1
HTA10_05_092	1	1	1
HTA10_05_095	1	1	1
HTA10_05_098	1	1	1
HTA10_05_103	1	1	1
HTA10_05_104	1	1	1
HTA10_05_105	1	1	1
HTA10_05_106	1	0	0
HTA10_06_002	1	1	1
HTA10_06_004	1	1	1
HTA10_06_005	1	1	1
HTA10_06_024	1	1	1
HTA10_06_025	1	1	1
HTA10_06_032	1	1	1
HTA10_06_043	1	1	1
HTA10_06_044	1	1	1
HTA10_06_045	1	1	1
HTA10_06_049	1	1	1
HTA10_06_051	1	1	1
HTA10_06_055	1	1	1
HTA10_06_061	1	1	1
HTA10_06_062	1	1	1
HTA10_06_065	1	1	1
HTA10_06_105	1	1	1
HTA10_06_107	1	1	1
HTA10_06_110	1	1	1
HTA10_07_001	1	1	1
HTA10_07_006	1	1	1
HTA10_07_101	1	1	1
HTA10_07_201	1	1	1
HTA10_07_301	1	0	0
HTA10_07_401	1	0	0
HTA10_07_406	1	0	0
HTA10_07_501	1	0	0
HTA10_EXT0_000	1	0	0

	Counts
10xVisiumSpatialTranscriptomics-RNA-seqLevel1	0
10xVisiumSpatialTranscriptomics-RNA-seqLevel2	0
10xVisiumSpatialTranscriptomics-AuxiliaryFiles	0
10xVisiumSpatialTranscriptomics-RNA-seqLevel3	0
10xVisiumSpatialTranscriptomics-RNA-seqLevel4	0
Slide-seqLevel1	0
Slide-seqLevel2	0
Slide-seqLevel3	0
ElectronMicroscopyLevel1	0
ElectronMicroscopyLevel2	0
ElectronMicroscopyLevel3	0
ElectronMicroscopyLevel4	0
MassSpectrometryLevel1	101
MassSpectrometryLevel2	0
MassSpectrometryLevel3	93
MassSpectrometryLevel4	93
MassSpectrometryAuxiliaryFile	0
RPPALevel1	0
RPPALevel2	0
RPPALevel3	0
RPPALevel4	0
OtherAssay	0
ExSeqMinimal	0
AccessoryManifest	0

gantt dateFormat X axisFormat %s section HTA10_01 Ascending colon Surgical Resection (10):milestone,0,0 section HTA10_01 Blood Blood draw:milestone,0,0 section HTA10_01 Descending colon Surgical Resection (12):milestone,0,0 section HTA10_01 Transverse colon Surgical Resection (9):milestone,0,0 section HTA10_02 Ascending colon Surgical Resection (10):milestone,0,0 section HTA10_02 Blood Blood draw:milestone,0,0 section HTA10_02 Descending colon Surgical Resection (14):milestone,0,0 section HTA10_02 Transverse colon Surgical Resection (10):milestone,0,0 section HTA10_03 Ascending colon Surgical Resection (2):milestone,0,0 section HTA10_03 Blood Blood draw:milestone,0,0 section HTA10_03 Descending colon Surgical Resection (12):milestone,0,0 section HTA10_03 Rectum NOS Surgical Resection (6):milestone,0,0 section HTA10_03 Transverse colon Surgical Resection (5):milestone,0,0 section HTA10_04 Ascending colon Surgical Resection (6):milestone,0,0 section HTA10_04 Blood Blood draw (2):milestone,0,0 section HTA10_04 Descending colon Surgical Resection (2):milestone,0,0 section HTA10_04 Rectum NOS Surgical Resection (5):milestone,0,0 section HTA10_04 Transverse colon Surgical Resection (4):milestone,0,0 section HTA10_05 Ascending colon Surgical Resection (9):milestone,0,0 section HTA10_05 Blood Blood draw:milestone,0,0 section HTA10_05 Colon NOS Surgical Resection:milestone,0,0 section HTA10_05 Descending colon Surgical Resection (10):milestone,0,0 section HTA10_05 Rectum NOS Surgical Resection (12):milestone,0,0 section HTA10_05 Transverse colon Surgical Resection (13):milestone,0,0 section HTA10_06 Ascending colon Surgical Resection (10):milestone,0,0 section HTA10_06 Ascending colon Surgical Resection:milestone,1545,1545 section HTA10_06 Blood Blood draw:milestone,0,0 section HTA10_06 Colon NOS Surgical Resection (2):milestone,0,0 section HTA10_06 Colon NOS Surgical Resection:milestone,1545,1545 section HTA10_06 Descending colon Surgical Resection (13):milestone,0,0 section HTA10_06 Sigmoid colon Surgical Resection:milestone,0,0 section HTA10_06 Transverse colon Surgical Resection (12):milestone,0,0 section HTA10_07 Ascending colon Surgical Resection:milestone,0,0 section HTA10_07 Descending colon Surgical Resection:milestone,0,0 section HTA10_07 Duodenum Surgical Resection:milestone,0,0 section HTA10_07 Ileum Surgical Resection:milestone,0,0 section HTA10_07 Jejunum Surgical Resection (2):milestone,0,0 section HTA10_07 Sigmoid colon Surgical Resection:milestone,0,0 section HTA10_07 Transverse colon Surgical Resection:milestone,0,0 section HTA10_08 Ascending colon Excision:milestone,0,0 section HTA10_08 Descending colon Excision:milestone,0,0 section HTA10_09 Rectum NOS Surgical Resection:milestone,0,0 section HTA10_10 Ascending colon Excision (2):milestone,0,0 section HTA10_11 Rectum NOS Surgical Resection:milestone,0,0 section HTA10_12 Rectum NOS Surgical Resection:milestone,0,0 section HTA10_13 Rectum NOS Surgical Resection:milestone,0,0 section HTA10_15 Descending colon Surgical Resection (2):milestone,0,0 section HTA10_16 Transverse colon Surgical Resection (4):milestone,0,0 section HTA10_17 Sigmoid colon Excision (2):milestone,0,0 section HTA10_18 Ascending colon Excision:milestone,0,0 section HTA10_18 Ascending colon Excision:milestone,5,5 section HTA10_18 Transverse colon Excision:milestone,0,0 section HTA10_18 Transverse colon Excision:milestone,5,5 section HTA10_19 Rectum NOS Excision:milestone,0,0 section HTA10_20 Ascending colon Excision (2):milestone,0,0 section HTA10_20 Cecum Excision:milestone,0,0 section HTA10_20 Descending colon Excision:milestone,0,0 section HTA10_20 Sigmoid colon Excision (4):milestone,0,0 section HTA10_20 Sigmoid colon Excision:milestone,245,245 section HTA10_21 Rectum NOS Excision:milestone,0,0 section HTA10_21 Sigmoid colon Excision:milestone,0,0 section HTA10_22 Ascending colon Excision:milestone,0,0 section HTA10_23 Ascending colon Surgical Resection (3):milestone,0,0 section HTA10_23 Descending colon Surgical Resection:milestone,0,0 section HTA10_23 Transverse colon Surgical Resection:milestone,0,0 section HTA10_24 Colon NOS Surgical Resection:milestone,0,0 section HTA10_25 Liver Surgical Resection:milestone,0,0 section HTA10_26 Ovary Surgical Resection:milestone,0,0 section HTA10_27 Sigmoid colon Surgical Resection:milestone,0,0 section HTA10_28 Colon NOS Surgical Resection:milestone,0,0 section HTA10_29 Cecum Surgical Resection:milestone,0,0 section HTA10_30 Transverse colon Surgical Resection:milestone,0,0 section HTA10_31 Cecum Surgical Resection:milestone,0,0 section HTA10_32 Cecum Surgical Resection:milestone,0,0 section HTA10_33 Sigmoid colon Surgical Resection:milestone,0,0 section HTA10_34 Descending colon Surgical Resection:milestone,0,0 section HTA10_34 Descending colon Surgical Resection (2):milestone,1,1 section HTA10_34 Transverse colon Surgical Resection:milestone,0,0 section HTA10_35 Descending colon Excision:milestone,0,0 section HTA10_36 Duodenum Excision:milestone,0,0 section HTA10_37 Descending colon Surgical Resection (2):milestone,0,0 section HTA10_38 Descending colon Surgical Resection (2):milestone,0,0 section HTA10_38 Duodenum Surgical Resection:milestone,0,0 section HTA10_38 Jejunum Surgical Resection (2):milestone,0,0 section HTA10_39 Descending colon Surgical Resection:milestone,0,0 section HTA10_40 Transverse colon Surgical Resection:milestone,0,0 section HTA10_41 Ascending colon Excision (2):milestone,0,0 section HTA10_41 Descending colon Excision:milestone,0,0 section HTA10_EXT0 unknown Other Acquisition Method:milestone,0,0

This tab is for HTAN DCC debugging purposes only. It reviews all paths in the atlas, and summarizes:

the number of files annotated via an existing metadata file.
the number of files upload to the cloud, but not yet annotated with any metadata.

Root Path	Num Annotated Files	Num Unannotated Files
bulkATACseq_level_1	46	0
bulkATACseq_level_2	23	23
bulkATACseq_level_3	0	46
bulkRNAseq	348	0
bulkRNAseq_level_1	72	0
bulkRNAseq_level_2	36	0
bulk_methyl_seq_level_1	80	0
bulk_methyl_seq_level_2	0	51
codex_level_1	16	0
codex_level_2	71	110
codex_level_3	1599	1
codex_level_4	70	26
HandE_Xenium_level_1	32	0
hic_level_1	66	0
hic_level_2	34	0
hic_level_3	2	0
lipidomics	214	0
metabolomics	494	0
proteomics_level_1	479	1
proteomics_level_3	28	1
proteomics_level_4	28	0
scatacseq_level_1	640	0
scatacseq_level_2	17	22
scatacseq_level_3	160	0
scrnaseq_level_1	384	1
scrnaseq_level_2	128	0
scrnaseq_level_3	192	0
stereoseq_level_4	0	3
wes_level_1	126	0
wes_level_2	51	51
wgs_level_1	506	0
wgs_level_2	108	108
wgs_longread_level_1	0	7
wgs_longread_level_3	0	3
Xenium	32	0

This tab is for HTAN DCC debugging purposes only. Atlases should please ignore.

Download Cytoscape SIF Network (DCC Debugging)

HTA10: HTAN Stanford

Total File Size

55.3 TB

Total Number of Files

6,536

Validation Errors

21

Percent Metadata Complete

59.9%

Clinical Data Matrix: Tiers 1 and 2

Clinical Data Matrix: Tier 3

Assay Matrix: Single Cell Data

Assay Matrix: Bulk Data

Assay Matrix: Core Imaging

Assay Matrix: Other

Longitudinal Data

Longitudinal Details Plot

HTA10: HTAN Stanford

Total File Size

55.3 TB

Total Number of Files

6,536

Validation Errors

21

Percent Metadata Complete

59.9%

All Atlas Categories are supported by the Dashboard. Failed: 2 errors

At least one Demographics file found. Passed

Non-Demographic clinical data use same IDs as demographics file. Passed

At least one Biospecimen file found. Passed

HTAN IDs follow the SOP. Passed

Links connect. Passed

Synapse Entity IDs are Specified for Assays. Passed

File names follow Cancer Data Service (CDS) conventions. Failed: 19 warnings

Clinical Data Matrix: Tiers 1 and 2

View Details

Clinical Data Matrix: Tier 3

View Details

Assay Matrix: Single Cell Data

View Details

Assay Matrix: Bulk Data

View Details

Assay Matrix: Core Imaging

View Details

Assay Matrix: Other

View Details

Longitudinal Data

Longitudinal Data

Longitudinal Details Plot

Longitudinal Details Plot