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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
395
total RNA-seq
164
ChIP-seq
153
ATAC-seq
80
single cell RNA-seq
51
WGBS
11
snATAC-seq
10
MeRIP-seq
9
Hi-C
8
DNase-seq
2
Capture-C
2
FAIRE-seq
2
RRBS
2
small RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
pCHi-C
Assay category
477
Transcription
174
DNA accessibility
164
DNA binding
53
DNA methylation
9
3D chromatin structure
Target of assay
120
histone
120
histone modification
61
narrow histone mark
59
broad histone mark
41
control
8
transcription factor
5
nucleotide modification
3
RNA binding protein
Date released
188
August, 2017
157
July, 2018
104
May, 2022
72
September, 2018
58
May, 2021
56
February, 2023
55
November, 2019
October, 2018
39
April, 2018
32
February, 2021
19
October, 2019
19
September, 2020
14
March, 2020
11
September, 2017
10
November, 2020
8
January, 2021
7
August, 2020
7
November, 2018
6
July, 2019
5
March, 2019
5
October, 2017
4
August, 2021
4
June, 2019
3
August, 2018
3
October, 2022
2
May, 2019
1
August, 2022
1
February, 2020
1
June, 2018
Available data
633
bam
579
bigWig
434
fastq
415
tsv
172
bed narrowPeak
80
zippedFastqFolder
51
bigBed narrowPeak
29
bed bed3+
21
bed broadPeak
16
tagAlign
7
bedpe bed3+
7
bigBed broadPeak
7
hic
6
bed bedMethyl
6
bigBed bedMethyl
6
txt
3
cool
1
bedpe
1
hdf5
Organism
883
Homo sapiens
Biosample type
455
tissue
344
primary cell
92
cell line
in vitro differentiated cells
Organ
890
pancreas
771
liver
564
connective tissue
492
epithelium
467
adipose tissue
392
heart
351
kidney
286
brain
236
vasculature
230
blood vessel
159
bone element
141
artery
122
limb
96
musculature of body
69
blood
69
bodily fluid
61
eye
43
nerve
25
spleen
22
vein
20
lung
18
ureter
16
skeleton
8
embryo
5
gonad
5
ovary
2
intestine
2
pericardium
2
pituitary gland
2
thymus
1
adrenal gland
1
bone marrow
1
esophagus
1
large intestine
1
lymph node
1
mammary gland
1
skin of body
1
small intestine
1
spinal cord
1
stomach
1
urinary bladder
Project
705
AMP
152
HPAP
34
T1D
Genome assembly (visualization)
614
hg19
591
GRCh38
Lab
670
AMP-T2D consortium
152
Klaus Kaestner, Upenn
51
Kyle Gaulton, UCSD
10
Rohit N. Kulkarni, M.D., Ph.D.
4
Bing Ren, UCSD
2
Mark McCarthy, Oxford
1
Maike Sander, UCSD
1
Stephen Parker, UMich
Audit category:
81
inconsistent ontology term
4
audit script error
Audit category:
54
missing controlled_by
Audit category:
8
inconsistent control read length
2
inconsistent assembly
biosample_type!
in vitro differentiated cells
month_released!
December, 2019
October, 2018
BIOSAMPLE
ASSAY
891 results
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total RNA-seq
ChIP-seq
ATAC-seq
single cell RNA-seq
WGBS
snATAC-seq
MeRIP-seq
Hi-C
DNase-seq
Capture-C
FAIRE-seq
RRBS
small RNA-seq
CRISPR genome editing followed by sgRNA sequencing
pCHi-C
tissue
islet of Langerhans
278
50
59
6
7
4
3
1
1
1
pancreas
2
14
2
4
1
2
1
1
1
body of pancreas
3
2
4
2
4
2
primary cell
pancreatic alpha cell
52
13
35
12
31
1
pancreatic beta cell
21
13
23
12
16
1
pancreatic acinar cell
2
8
9
12
1
pancreatic ductal cell
4
13
4
10
pancreatic endocrine cell
23
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cell line
EndoC_BH1
33
15
19
6
1
2
1
Panc1
13
1
1
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