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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
1053
total RNA-seq
936
ChIP-seq
180
DNase-seq
160
ATAC-seq
113
single cell RNA-seq
87
RNA microarray
30
pCHi-C
28
WGBS
16
Hi-C
16
small RNA-seq
11
RRBS
4
FAIRE-seq
3
snDrop-seq
2
Capture-C
2
snATAC-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
Assay category
1182
Transcription
936
DNA binding
346
DNA accessibility
39
DNA methylation
16
3D chromatin structure
Target of assay
543
histone modification
542
histone
291
narrow histone mark
251
broad histone mark
198
transcription factor
193
control
53
RNA binding protein
23
recombinant protein
17
chromatin remodeller
3
other context
3
other post-translational modification
Date released
641
February, 2021
November, 2017
284
August, 2017
272
October, 2019
194
May, 2020
163
June, 2019
120
July, 2018
115
May, 2019
109
August, 2021
87
November, 2018
80
April, 2019
78
February, 2023
77
July, 2019
74
October, 2018
59
May, 2021
56
November, 2019
51
March, 2020
48
December, 2017
35
December, 2018
30
January, 2019
25
February, 2020
22
October, 2017
6
April, 2018
6
September, 2017
3
December, 2019
3
January, 2018
2
May, 2022
1
August, 2022
1
May, 2023
1
October, 2022
Available data
2081
bam
1894
bigWig
1185
tsv
925
bed narrowPeak
610
bigBed narrowPeak
463
fastq
208
bed bed3+
206
bed broadPeak
180
tagAlign
177
bigBed broadPeak
95
txt
26
bed bedMethyl
26
bigBed bedMethyl
10
bedpe bed3+
10
hic
6
bed bed3
6
csv
1
hdf5
1
tagAlign bed3+
Organism
2633
Homo sapiens
Biosample type
2343
tissue
515
primary cell
340
in vitro differentiated cells
300
cell line
8
stem cell
Organ
547
connective tissue
528
pancreas
488
adipose tissue
376
liver
339
heart
199
blood vessel
199
vasculature
183
brain
158
bone element
139
artery
127
kidney
122
limb
88
epithelium
82
musculature of body
61
blood
61
bodily fluid
56
eye
43
nerve
25
spleen
18
ureter
16
skeleton
8
embryo
5
gonad
5
ovary
2
intestine
2
pituitary gland
1
adrenal gland
1
esophagus
1
large intestine
1
lung
1
lymph node
1
mammary gland
1
pericardium
1
skin of body
1
small intestine
1
spinal cord
1
stomach
1
thymus
1
urinary bladder
Project
2635
AMP
8
T1D
Genome assembly (visualization)
1955
hg19
1931
GRCh38
Lab
2643
AMP-T2D consortium
142
Katalin Susztak, Upenn
57
Kyle Gaulton, UCSD
47
KPMP
40
Karen Mohlke, UNC
40
Patrick T. Ellinor, Broad
37
Bing Ren, UCSD
19
Xin Sun, UCSD
10
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
2
Mark McCarthy, Oxford
1
Maike Sander, UCSD
1
Stephen Parker, UMich
Audit category:
176
inconsistent ontology term
28
inconsistent control
9
audit script error
1
inconsistent replicate
Audit category:
29
missing controlled_by
Audit category:
11
inconsistent control read length
4
inconsistent control run_type
2
inconsistent assembly
files.file_type!
bedpe
month_released!
November, 2017
BIOSAMPLE
ASSAY
2643 results
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total RNA-seq
ChIP-seq
DNase-seq
ATAC-seq
single cell RNA-seq
RNA microarray
pCHi-C
WGBS
Hi-C
small RNA-seq
RRBS
FAIRE-seq
snDrop-seq
Capture-C
snATAC-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
tissue
islet of Langerhans
280
71
1
34
6
4
1
1
1
1
adipose tissue
382
2
3
1
3
liver
147
145
2
1
1
3
1
1
1
bone element
84
heart left ventricle
3
35
3
2
18
1
4
1
1
+ See 174 more…
cell line
EndoC_BH1
33
15
19
1
2
1
smooth muscle cell of the coronary artery
52
6
8
GM12878
60
1
HepG2
5
45
1
2
1
1
Panc1
13
1
1
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