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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
422
ChIP-seq
108
total RNA-seq
28
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
422
DNA binding
110
Transcription
30
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
310
transcription factor
89
recombinant protein
77
control
55
RNA binding protein
37
histone
37
histone modification
20
chromatin remodeller
19
broad histone mark
18
narrow histone mark
3
nucleotide modification
2
other context
other post-translational modification
Date released
313
November, 2017
96
February, 2021
46
November, 2018
44
August, 2021
30
October, 2019
21
May, 2021
16
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
January, 2019
2
March, 2023
1
December, 2018
1
May, 2020
1
October, 2022
Available data
515
bam
460
bigWig
360
fastq
348
bed narrowPeak
299
bigBed narrowPeak
114
tsv
58
bed broadPeak
58
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
590
Homo sapiens
Biosample type
2767
tissue
1080
primary cell
594
cell line
394
in vitro differentiated cells
10
stem cell
Organ
394
liver
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
blood
43
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
583
AMP
9
T1D
2
community
Genome assembly (visualization)
468
hg19
403
GRCh38
Lab
547
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
92
inconsistent ontology term
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
target.investigated_as!
other post-translational modification
month_released!
January, 2019
organ_slims!
blood
BIOSAMPLE
ASSAY
594 results
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ChIP-seq
total RNA-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
376
9
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
Panc1
13
1
1
H1-hESC
8
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