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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
622
ChIP-seq
249
total RNA-seq
70
ATAC-seq
11
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
3
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
622
DNA binding
253
Transcription
73
DNA accessibility
8
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
359
transcription factor
149
histone
149
histone modification
114
control
89
recombinant protein
75
broad histone mark
73
narrow histone mark
66
RNA binding protein
23
chromatin remodeller
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
153
May, 2021
122
February, 2021
86
August, 2021
68
August, 2017
46
November, 2018
43
December, 2017
39
February, 2018
38
October, 2019
22
February, 2023
21
November, 2019
19
March, 2020
6
November, 2020
5
January, 2019
4
January, 2018
2
December, 2019
2
March, 2023
1
August, 2018
1
December, 2018
1
May, 2020
1
October, 2022
Available data
813
bam
726
bigWig
508
fastq
482
bed narrowPeak
318
bigBed narrowPeak
250
tsv
60
bed broadPeak
60
bigBed broadPeak
60
tagAlign
28
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
991
Homo sapiens
Biosample type
2737
tissue
1080
primary cell
601
cell line
394
in vitro differentiated cells
10
stem cell
Organ
416
liver
103
epithelium
97
connective tissue
95
pancreas
67
heart
66
artery
66
blood vessel
66
vasculature
61
blood
bodily fluid
37
embryo
19
kidney
1
adipose tissue
1
mammary gland
Project
984
AMP
9
T1D
2
community
Genome assembly (visualization)
772
hg19
675
GRCh38
4
hg18
Lab
894
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:
19
missing controlled_by
Audit category:
43
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
organ_slims!
bodily fluid
BIOSAMPLE
ASSAY
995 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
DNase-seq
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
378
14
1
2
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
Panc1
13
1
1
H1-hESC
8
+ See 13 more…
in vitro differentiated cells
adipocyte
67
5
8
1
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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