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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
123
ChIP-seq
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
2
HiChIP
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
123
DNA binding
31
DNA accessibility
4
3D chromatin structure
2
Transcription
1
DNA methylation
1
DNA sequencing
Target of assay
transcription factor
89
recombinant protein
83
control
65
RNA binding protein
38
histone
38
histone modification
30
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
74
November, 2017
19
October, 2019
17
May, 2021
16
August, 2021
14
November, 2019
13
February, 2021
7
March, 2020
6
February, 2023
6
November, 2020
4
January, 2019
4
November, 2018
3
December, 2018
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
129
bam
85
fastq
62
bigWig
52
bed narrowPeak
27
bigBed narrowPeak
15
bed broadPeak
15
bigBed broadPeak
15
tagAlign
6
tsv
3
bed bed3+
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
184
Homo sapiens
Biosample type
1611
tissue
831
primary cell
209
in vitro differentiated cells
188
cell line
10
stem cell
Organ
90
liver
58
pancreas
44
epithelium
10
artery
10
blood
10
blood vessel
10
bodily fluid
10
heart
10
vasculature
8
kidney
1
mammary gland
Project
179
AMP
7
T1D
2
community
Genome assembly (visualization)
74
hg19
51
GRCh38
Lab
161
AMP-T2D consortium
14
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
48
inconsistent ontology term
1
inconsistent replicate
Audit category:
1
missing controlled_by
Audit category:
11
inconsistent control read length
1
inconsistent assembly
assay_title!
total RNA-seq
target.investigated_as!
transcription factor
BIOSAMPLE
ASSAY
188 results
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ChIP-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
81
1
2
2
2
1
1
EndoC_BH1
14
19
6
1
3
2
2
1
Panc1
13
1
1
GM12878
9
1
smooth muscle cell of the coronary artery
2
8
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