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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
376
ChIP-seq
113
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
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
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
376
DNA binding
115
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
recombinant protein
83
control
65
RNA binding protein
38
histone
38
histone modification
30
chromatin remodeller
19
broad histone mark
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
242
November, 2017
96
February, 2021
45
November, 2018
42
August, 2021
28
December, 2018
22
January, 2019
20
May, 2021
20
October, 2019
12
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
476
bam
415
bigWig
337
fastq
298
bed narrowPeak
264
bigBed narrowPeak
119
tsv
53
bed broadPeak
53
bigBed broadPeak
15
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
550
Homo sapiens
Biosample type
2428
tissue
973
primary cell
554
cell line
339
in vitro differentiated cells
9
stem cell
Organ
310
liver
83
pancreas
73
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
60
blood
60
bodily fluid
12
kidney
8
embryo
1
mammary gland
Project
545
AMP
7
T1D
2
community
Genome assembly (visualization)
426
hg19
360
GRCh38
Lab
509
AMP-T2D consortium
32
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
79
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
11
missing controlled_by
Audit category:
20
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
target.investigated_as!
recombinant protein
narrow histone mark
BIOSAMPLE
ASSAY
554 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
287
14
1
2
2
2
1
1
EndoC_BH1
9
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
59
1
Panc1
10
1
1
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