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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
443
ChIP-seq
79
total RNA-seq
10
ATAC-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
HiChIP
1
DNase-seq
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
443
DNA binding
81
Transcription
11
DNA accessibility
3
3D chromatin structure
1
DNA sequencing
Target of assay
360
transcription factor
89
recombinant protein
78
control
64
RNA binding protein
30
chromatin remodeller
histone
26
histone modification
13
broad histone mark
13
narrow histone mark
2
other context
2
other post-translational modification
Date released
300
November, 2017
70
February, 2021
60
November, 2018
39
August, 2021
28
December, 2018
22
January, 2019
21
October, 2019
6
March, 2020
5
February, 2023
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
508
bam
447
bigWig
411
fastq
366
bed narrowPeak
334
bigBed narrowPeak
84
tsv
45
bed broadPeak
45
bigBed broadPeak
9
tagAlign
3
bed bed3+
3
tar
1
bed bed3
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
1
vcf
Organism
553
Homo sapiens
Biosample type
2110
tissue
556
cell line
507
primary cell
273
in vitro differentiated cells
8
stem cell
Organ
382
liver
73
pancreas
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
60
blood
60
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
549
AMP
5
T1D
2
community
Genome assembly (visualization)
453
hg19
394
GRCh38
Lab
518
AMP-T2D consortium
31
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
16
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
files.file_type!
bed bedMethyl
organ_slims!
epithelium
target.investigated_as!
histone
BIOSAMPLE
ASSAY
556 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
HiChIP
DNase-seq
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
360
14
1
2
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
59
1
H1-hESC
8
Panc1
6
1
1
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