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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
504
ChIP-seq
249
total RNA-seq
67
ATAC-seq
10
pCHi-C
7
Hi-C
6
MeRIP-seq
5
STARR-seq
4
GRO-seq
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
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
504
DNA binding
253
Transcription
69
DNA accessibility
7
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
387
transcription factor
histone
140
histone modification
115
control
88
recombinant protein
74
RNA binding protein
71
broad histone mark
68
narrow histone mark
27
chromatin remodeller
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
291
November, 2017
131
May, 2021
121
February, 2021
67
August, 2021
58
November, 2018
29
October, 2019
28
December, 2018
23
February, 2018
22
January, 2019
19
August, 2017
18
February, 2023
18
March, 2020
15
December, 2017
11
November, 2019
6
November, 2020
5
January, 2018
2
December, 2019
2
March, 2023
1
August, 2018
1
May, 2020
1
October, 2022
Available data
742
bam
650
bigWig
470
fastq
412
bed narrowPeak
329
bigBed narrowPeak
250
tsv
46
bed broadPeak
46
bigBed broadPeak
23
tagAlign
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
865
Homo sapiens
Biosample type
1949
tissue
817
primary cell
609
cell line
260
in vitro differentiated cells
7
stem cell
Organ
373
liver
76
epithelium
73
pancreas
67
heart
66
artery
66
blood vessel
66
vasculature
60
blood
60
bodily fluid
42
connective tissue
24
embryo
19
kidney
1
adipose tissue
1
mammary gland
Project
860
AMP
7
T1D
2
community
Genome assembly (visualization)
677
hg19
597
GRCh38
4
hg18
Lab
793
AMP-T2D consortium
32
Kyle Gaulton, UCSD
31
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Struan F.A. Grant, CHOP
2
Anna Gloyn, Oxford
Audit category:
191
inconsistent ontology term
2
audit script error
1
inconsistent control
1
inconsistent replicate
Audit category:
missing controlled_by
Audit category:
16
inconsistent control read length
2
inconsistent control run_type
audit.NOT_COMPLIANT.category!
missing controlled_by
files.file_type!
bed bed3+
target.investigated_as!
histone
BIOSAMPLE
ASSAY
869 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
Hi-C
MeRIP-seq
STARR-seq
GRO-seq
CRISPR genome editing followed by DNA sequencing
Capture-C
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
348
14
1
1
2
2
1
1
EndoC_BH1
3
33
19
1
6
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
59
1
H1-hESC
8
+ See 14 more…
in vitro differentiated cells
cardiomyocytes
3
59
embryonic stem cell
18
7
6
1
adipocyte
18
5
7
1
neural progenitor cell
7
7
10
cardiac precursors (cardiac muscle cell)
19
1
1
+ See 31 more…
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