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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
110
ChIP-seq
61
total RNA-seq
21
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
110
DNA binding
63
Transcription
23
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
transcription factor
88
recombinant protein
81
control
59
RNA binding protein
27
histone
27
histone modification
19
chromatin remodeller
14
narrow histone mark
13
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
63
November, 2017
33
August, 2021
29
February, 2021
23
October, 2019
21
May, 2021
15
November, 2019
11
March, 2020
9
January, 2019
6
February, 2023
6
November, 2020
4
November, 2018
3
December, 2018
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
160
bam
103
bigWig
79
fastq
67
tsv
35
bed narrowPeak
18
bigBed narrowPeak
4
bed broadPeak
4
bigBed broadPeak
3
bed bed3+
2
bedpe bed3+
2
hic
2
tagAlign
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
224
Homo sapiens
Biosample type
2547
tissue
1043
primary cell
301
in vitro differentiated cells
228
cell line
8
stem cell
Organ
93
liver
91
pancreas
78
epithelium
62
artery
blood vessel
62
heart
62
vasculature
12
kidney
10
blood
10
bodily fluid
8
embryo
1
mammary gland
Project
217
AMP
9
T1D
2
community
Genome assembly (visualization)
107
hg19
86
GRCh38
Lab
192
AMP-T2D consortium
23
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
84
inconsistent ontology term
1
inconsistent replicate
Audit category:
1
missing controlled_by
Audit category:
inconsistent control read length
1
inconsistent assembly
audit.WARNING.category!
inconsistent control read length
month_released!
February, 2018
organ_slims!
blood vessel
target.investigated_as!
transcription factor
BIOSAMPLE
ASSAY
228 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
70
14
1
2
2
2
1
1
EndoC_BH1
14
33
19
6
1
3
2
2
1
Panc1
13
1
1
GM12878
9
1
H1-hESC
8
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