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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
113
total RNA-seq
97
ChIP-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
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
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
115
Transcription
97
DNA binding
31
DNA accessibility
3D chromatin structure
1
DNA sequencing
Target of assay
63
transcription factor
24
control
23
histone
23
histone modification
narrow histone mark
11
broad histone mark
10
RNA binding protein
8
chromatin remodeller
7
recombinant protein
3
nucleotide modification
Date released
November, 2017
96
February, 2021
November, 2018
41
August, 2021
27
December, 2018
26
October, 2019
22
January, 2019
20
May, 2021
11
November, 2019
10
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
197
bam
184
bigWig
119
tsv
87
bed narrowPeak
49
fastq
46
bigBed narrowPeak
8
tagAlign
2
bed bed3+
1
bed bed3
1
bed broadPeak
1
bigBed broadPeak
1
txt
1
vcf
Organism
266
Homo sapiens
Biosample type
2357
tissue
956
primary cell
335
in vitro differentiated cells
270
cell line
9
stem cell
Organ
81
pancreas
72
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
45
blood
45
bodily fluid
36
liver
19
kidney
8
embryo
1
mammary gland
Project
261
AMP
7
T1D
2
community
Genome assembly (visualization)
195
hg19
179
GRCh38
Lab
226
AMP-T2D consortium
31
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
85
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
assay_slims!
3D chromatin structure
month_released!
November, 2017
November, 2018
target.investigated_as!
narrow histone mark
BIOSAMPLE
ASSAY
270 results
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total RNA-seq
ChIP-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
EndoC_BH1
33
9
19
6
3
2
2
1
smooth muscle cell of the coronary artery
52
6
8
GM12878
44
1
HepG2
14
16
1
2
2
1
Panc1
10
1
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