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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
649
ChIP-seq
249
total RNA-seq
71
ATAC-seq
10
pCHi-C
8
Hi-C
6
MeRIP-seq
5
STARR-seq
4
Capture-C
4
GRO-seq
3
CRISPR genome editing followed by DNA sequencing
DNase-seq
2
HiChIP
2
single cell RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
649
DNA binding
253
Transcription
71
DNA accessibility
8
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
410
transcription factor
150
histone
150
histone modification
120
control
89
recombinant protein
76
RNA binding protein
75
broad histone mark
74
narrow histone mark
chromatin remodeller
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
300
November, 2017
153
May, 2021
122
February, 2021
86
August, 2021
65
August, 2017
54
November, 2018
42
December, 2017
39
February, 2018
36
October, 2019
26
December, 2018
22
February, 2023
21
November, 2019
19
March, 2020
17
January, 2019
6
November, 2020
5
January, 2018
2
December, 2019
2
March, 2023
1
August, 2018
May, 2020
1
October, 2022
Available data
837
bam
745
bigWig
534
fastq
500
bed narrowPeak
338
bigBed narrowPeak
249
tsv
60
tagAlign
54
bed broadPeak
54
bigBed broadPeak
27
bed bed3+
9
bedpe bed3+
7
bed bedgraph
6
bed bed3
6
hic
4
txt
3
tar
2
ibed
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
vcf
Organism
1015
Homo sapiens
Biosample type
2404
tissue
909
primary cell
629
cell line
390
in vitro differentiated cells
10
stem cell
Organ
394
liver
101
epithelium
94
connective tissue
94
pancreas
67
heart
66
artery
66
blood vessel
66
vasculature
51
blood
51
bodily fluid
37
embryo
18
kidney
1
adipose tissue
1
mammary gland
Project
1008
AMP
9
T1D
2
community
Genome assembly (visualization)
791
hg19
695
GRCh38
4
hg18
Lab
918
AMP-T2D consortium
52
Kyle Gaulton, UCSD
34
Bing Ren, UCSD
7
Struan F.A. Grant, CHOP
6
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
Audit category:
207
inconsistent ontology term
2
audit script error
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
30
inconsistent control read length
1
inconsistent assembly
assay_title!
DNase-seq
month_released!
May, 2020
target.investigated_as!
chromatin remodeller
BIOSAMPLE
ASSAY
1019 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
Hi-C
MeRIP-seq
STARR-seq
Capture-C
GRO-seq
CRISPR genome editing followed by DNA sequencing
HiChIP
single cell RNA-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
358
14
1
1
2
2
1
1
EndoC_BH1
15
33
19
1
6
2
3
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
50
1
Panc1
13
1
+ See 14 more…
in vitro differentiated cells
adipocyte
65
5
8
1
cardiomyocytes
3
59
embryonic stem cell
40
7
6
1
neural progenitor cell
21
7
10
pancreatic endoderm
18
4
1
+ See 31 more…
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