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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
1144
total RNA-seq
1048
ChIP-seq
289
ATAC-seq
180
DNase-seq
180
single cell RNA-seq
87
RNA microarray
31
pCHi-C
28
snATAC-seq
20
Hi-C
16
small RNA-seq
11
WGBS
10
MeRIP-seq
5
STARR-seq
4
FAIRE-seq
3
CRISPR genome editing followed by DNA sequencing
3
snDrop-seq
2
Capture-C
2
HiChIP
2
RRBS
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
1342
Transcription
1048
DNA binding
501
DNA accessibility
20
3D chromatin structure
13
DNA methylation
1
DNA sequencing
Target of assay
666
histone modification
665
histone
455
transcription factor
narrow histone mark
322
broad histone mark
270
control
93
RNA binding protein
89
recombinant protein
32
chromatin remodeller
5
nucleotide modification
5
other context
5
other post-translational modification
Date released
641
February, 2021
362
November, 2017
271
August, 2021
229
August, 2017
167
May, 2020
163
June, 2019
140
October, 2019
120
July, 2018
101
February, 2023
82
May, 2019
80
November, 2018
66
May, 2022
63
July, 2019
63
October, 2018
60
May, 2021
57
April, 2019
52
November, 2019
48
March, 2020
47
September, 2023
46
December, 2017
35
December, 2018
27
January, 2019
25
February, 2020
25
May, 2024
21
October, 2017
19
April, 2020
15
May, 2023
10
November, 2020
8
January, 2021
6
April, 2018
6
September, 2017
5
March, 2019
3
December, 2019
3
January, 2018
2
March, 2023
1
August, 2022
1
October, 2022
Available data
2229
bam
2007
bigWig
1195
tsv
1104
bed narrowPeak
798
bigBed narrowPeak
768
fastq
251
bed broadPeak
229
bigBed broadPeak
202
bed bed3+
158
txt
143
tagAlign
64
xls
bed bedMethyl
26
bigBed bedMethyl
13
hic
12
bedpe bed3+
6
bed bed3
6
csv
3
tar
1
bedpe
1
hdf5
1
vcf
Organism
3059
Homo sapiens
Biosample type
2428
tissue
963
primary cell
642
cell line
339
in vitro differentiated cells
9
stem cell
Organ
707
liver
550
pancreas
532
connective tissue
474
adipose tissue
334
heart
307
kidney
180
blood vessel
180
vasculature
158
bone element
150
brain
133
artery
106
limb
88
epithelium
70
musculature of body
60
blood
60
bodily fluid
54
eye
35
nerve
21
spleen
20
lung
18
ureter
16
skeleton
8
embryo
2
intestine
2
thymus
1
adrenal gland
1
esophagus
1
gonad
1
large intestine
1
mammary gland
1
ovary
1
pituitary gland
1
skin of body
1
small intestine
1
spinal cord
1
stomach
1
urinary bladder
Project
2966
AMP
47
KPMP
36
T1D
19
LungMap
2
community
Genome assembly (visualization)
2039
GRCh38
2018
hg19
Lab
2688
AMP-T2D consortium
142
Katalin Susztak, Upenn
57
Kyle Gaulton, UCSD
47
KPMP
40
Karen Mohlke, UNC
36
Bing Ren, UCSD
25
Patrick T. Ellinor, Broad
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:
175
inconsistent ontology term
28
inconsistent control
9
audit script error
1
inconsistent replicate
Audit category:
34
missing controlled_by
Audit category:
24
inconsistent control read length
8
inconsistent control run_type
2
inconsistent assembly
files.file_type!
bed bedMethyl
target.investigated_as!
narrow histone mark
BIOSAMPLE
ASSAY
3070 results
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Clear Filters
total RNA-seq
ChIP-seq
ATAC-seq
DNase-seq
single cell RNA-seq
RNA microarray
pCHi-C
snATAC-seq
Hi-C
small RNA-seq
WGBS
MeRIP-seq
STARR-seq
FAIRE-seq
CRISPR genome editing followed by DNA sequencing
snDrop-seq
Capture-C
HiChIP
RRBS
CRISPR genome editing followed by sgRNA sequencing
...and 4 more
tissue
islet of Langerhans
292
34
68
1
6
4
7
3
4
1
adipose tissue
382
1
3
1
1
liver
167
103
20
2
1
1
1
1
3
kidney
49
17
75
13
64
6
1
1
bone element
84
+ See 117 more…
cell line
HepG2
14
369
1
2
2
2
EndoC_BH1
33
9
19
1
6
3
2
2
1
smooth muscle cell of the coronary artery
52
6
8
GM12878
59
1
Panc1
10
1
1
+ See 14 more…
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