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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
104
ChIP-seq
77
total RNA-seq
10
ATAC-seq
4
STARR-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
2
DNase-seq
2
Hi-C
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
104
DNA binding
79
Transcription
12
DNA accessibility
2
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
transcription factor
82
recombinant protein
75
control
62
RNA binding protein
28
chromatin remodeller
26
histone
26
histone modification
13
broad histone mark
13
narrow histone mark
2
other context
2
other post-translational modification
Date released
74
November, 2017
65
February, 2021
30
August, 2021
17
October, 2019
9
January, 2019
6
February, 2023
4
March, 2020
4
November, 2018
December, 2018
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
177
bam
114
bigWig
87
fastq
80
tsv
37
bed narrowPeak
25
bigBed narrowPeak
15
bed broadPeak
15
bigBed broadPeak
15
tagAlign
3
bed bed3+
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
1
vcf
Organism
210
Homo sapiens
Biosample type
2583
tissue
1027
primary cell
233
in vitro differentiated cells
214
cell line
9
stem cell
Organ
103
liver
62
artery
62
blood vessel
62
heart
62
vasculature
16
pancreas
8
blood
8
bodily fluid
8
embryo
4
kidney
3
epithelium
1
mammary gland
Project
207
AMP
5
T1D
2
community
Genome assembly (visualization)
124
hg19
104
GRCh38
Lab
185
AMP-T2D consortium
22
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
inconsistent ontology term
1
inconsistent replicate
Audit category:
1
missing controlled_by
Audit category:
11
inconsistent control read length
1
inconsistent assembly
audit.ERROR.category!
inconsistent ontology term
month_released!
December, 2018
organ_slims!
gonad
target.investigated_as!
transcription factor
BIOSAMPLE
ASSAY
214 results
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ChIP-seq
total RNA-seq
ATAC-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
DNase-seq
Hi-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
81
14
1
2
2
1
1
1
smooth muscle cell of the coronary artery
2
52
8
Panc1
13
1
1
GM12878
7
1
H1-hESC
8
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