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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
229
total RNA-seq
142
ChIP-seq
71
ATAC-seq
10
pCHi-C
7
Hi-C
6
MeRIP-seq
5
STARR-seq
4
Capture-C
3
CRISPR genome editing followed by DNA sequencing
2
DNase-seq
2
HiChIP
2
single cell RNA-seq
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
233
Transcription
142
DNA binding
73
DNA accessibility
7
3D chromatin structure
1
DNA sequencing
Target of assay
69
histone
69
histone modification
40
transcription factor
36
broad histone mark
36
control
33
narrow histone mark
7
RNA binding protein
7
recombinant protein
3
nucleotide modification
Date released
153
May, 2021
122
February, 2021
86
August, 2021
38
October, 2019
22
February, 2023
21
November, 2019
19
March, 2020
14
August, 2017
6
November, 2020
2
December, 2019
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
873
bam
781
bigWig
fastq
536
bed narrowPeak
372
bigBed narrowPeak
250
tsv
60
bed broadPeak
60
bigBed broadPeak
60
tagAlign
28
bed bed3+
9
bedpe bed3+
7
bed bedgraph
6
bed bed3
6
hic
4
txt
3
tar
2
ibed
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
vcf
Organism
484
Homo sapiens
Biosample type
2336
tissue
679
primary cell
253
in vitro differentiated cells
235
cell line
6
stem cell
Organ
95
pancreas
84
epithelium
67
heart
66
artery
66
blood vessel
66
vasculature
42
connective tissue
34
liver
19
kidney
10
embryo
1
blood
1
bodily fluid
1
mammary gland
Project
477
AMP
9
T1D
2
community
Genome assembly (visualization)
342
hg19
290
GRCh38
Lab
387
AMP-T2D consortium
52
Kyle Gaulton, UCSD
34
Bing Ren, UCSD
7
Struan F.A. Grant, CHOP
6
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
Audit category:
203
inconsistent ontology term
2
audit script error
1
inconsistent replicate
Audit category:
1
inconsistent assembly
files.file_type!
fastq
xls
BIOSAMPLE
ASSAY
488 results
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Clear Filters
total RNA-seq
ChIP-seq
ATAC-seq
pCHi-C
Hi-C
MeRIP-seq
STARR-seq
Capture-C
CRISPR genome editing followed by DNA sequencing
DNase-seq
HiChIP
single cell RNA-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
in vitro differentiated cells
cardiomyocytes
59
3
embryonic stem cell
5
37
6
1
neural progenitor cell
7
21
10
adipocyte
5
14
8
1
cardiac precursors (cardiac muscle cell)
19
1
1
+ See 21 more…
cell line
EndoC_BH1
33
15
19
1
6
2
3
2
1
smooth muscle cell of the coronary artery
52
6
8
HepG2
9
18
1
2
1
2
1
Panc1
13
1
1
H1-hESC
8
+ See 14 more…
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