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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
99
total RNA-seq
96
ChIP-seq
28
ATAC-seq
6
MeRIP-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
STARR-seq
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
DNase-seq
1
Hi-C
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
Assay category
101
Transcription
96
DNA binding
29
DNA accessibility
1
3D chromatin structure
Target of assay
64
transcription factor
23
control
20
histone
20
histone modification
11
RNA binding protein
broad histone mark
10
chromatin remodeller
10
narrow histone mark
7
recombinant protein
3
nucleotide modification
Date released
94
February, 2021
27
December, 2018
24
October, 2019
21
May, 2021
18
January, 2019
15
November, 2018
13
August, 2021
11
March, 2020
10
November, 2019
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
October, 2022
Available data
206
bam
181
bigWig
104
tsv
87
bed narrowPeak
60
fastq
59
bigBed narrowPeak
8
tagAlign
bed bed3+
1
bed broadPeak
1
bedpe bed3+
1
bigBed broadPeak
1
hdf5
1
hic
1
txt
Organism
245
Homo sapiens
Biosample type
1945
tissue
922
primary cell
309
in vitro differentiated cells
249
cell line
7
stem cell
Organ
liver
80
pancreas
73
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
238
AMP
9
T1D
2
community
Genome assembly (visualization)
189
hg19
185
GRCh38
Lab
233
AMP-T2D consortium
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
3
Bing Ren, UCSD
2
Anna Gloyn, Oxford
Audit category:
86
inconsistent ontology term
1
inconsistent control
files.file_type!
bed bed3+
organ_slims!
liver
target.investigated_as!
broad histone mark
BIOSAMPLE
ASSAY
249 results
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total RNA-seq
ChIP-seq
ATAC-seq
MeRIP-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
STARR-seq
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
Hi-C
MPRA
shRNA RNA-seq
siRNA RNA-seq
cell line
EndoC_BH1
33
9
19
6
3
2
2
1
1
smooth muscle cell of the coronary artery
52
6
8
GM12878
60
1
Panc1
9
H1-hESC
8
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