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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
431
ChIP-seq
104
total RNA-seq
29
ATAC-seq
6
pCHi-C
3
Hi-C
2
Capture-C
2
DNase-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
Assay category
431
DNA binding
104
Transcription
31
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
350
transcription factor
89
recombinant protein
76
control
64
RNA binding protein
histone
35
histone modification
30
chromatin remodeller
18
broad histone mark
17
narrow histone mark
2
other context
2
other post-translational modification
Date released
300
November, 2017
96
February, 2021
61
November, 2018
28
December, 2018
23
October, 2019
22
January, 2019
20
May, 2021
10
August, 2021
10
March, 2020
6
November, 2019
1
February, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
547
bam
474
bigWig
411
fastq
358
bed narrowPeak
335
bigBed narrowPeak
110
tsv
45
bed broadPeak
45
bigBed broadPeak
9
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
Organism
578
Homo sapiens
Biosample type
1377
tissue
580
cell line
399
primary cell
247
in vitro differentiated cells
6
stem cell
Organ
355
liver
67
pancreas
66
artery
66
blood vessel
66
heart
66
vasculature
61
epithelium
60
blood
60
bodily fluid
17
kidney
8
embryo
1
mammary gland
Project
578
AMP
2
T1D
Genome assembly (visualization)
481
hg19
432
GRCh38
Lab
580
AMP-T2D consortium
31
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
Audit category:
73
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
12
missing controlled_by
Audit category:
15
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
month_released!
March, 2023
organ_slims!
adipose tissue
target.investigated_as!
histone
BIOSAMPLE
ASSAY
580 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
Hi-C
Capture-C
DNase-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
cell line
HepG2
345
5
1
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
59
1
EndoC_BH1
3
33
19
1
2
1
H1-hESC
8
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