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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
106
ChIP-seq
77
total RNA-seq
10
ATAC-seq
4
STARR-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
DNase-seq
2
HiChIP
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
106
DNA binding
79
Transcription
12
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
transcription factor
82
recombinant protein
75
control
64
RNA binding protein
30
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
5
February, 2023
4
March, 2020
4
November, 2018
3
December, 2018
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
179
bam
116
bigWig
90
fastq
80
tsv
39
bed narrowPeak
27
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
213
Homo sapiens
Biosample type
2592
tissue
1027
primary cell
233
in vitro differentiated cells
216
cell line
9
stem cell
Organ
104
liver
62
artery
62
blood vessel
62
heart
62
vasculature
15
pancreas
10
blood
10
bodily fluid
8
embryo
4
kidney
2
epithelium
1
mammary gland
Project
209
AMP
5
T1D
2
community
Genome assembly (visualization)
126
hg19
106
GRCh38
Lab
187
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
assay_title!
CRISPR genome editing followed by sgRNA sequencing
audit.ERROR.category!
inconsistent ontology term
target.investigated_as!
transcription factor
BIOSAMPLE
ASSAY
216 results
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ChIP-seq
total RNA-seq
ATAC-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
DNase-seq
HiChIP
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
81
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
2
52
8
Panc1
13
1
1
GM12878
9
1
H1-hESC
8
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