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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
442
ChIP-seq
108
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
442
DNA binding
110
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
347
transcription factor
89
recombinant protein
80
control
59
RNA binding protein
37
histone
37
histone modification
chromatin remodeller
19
broad histone mark
18
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
300
November, 2017
96
February, 2021
54
November, 2018
44
August, 2021
30
October, 2019
26
December, 2018
21
May, 2021
January, 2019
16
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
535
bam
478
bigWig
380
fastq
365
bed narrowPeak
316
bigBed narrowPeak
114
tsv
55
bed broadPeak
55
bigBed broadPeak
20
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
611
Homo sapiens
Biosample type
2728
tissue
1087
primary cell
615
cell line
391
in vitro differentiated cells
10
stem cell
Organ
376
liver
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
39
blood
39
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
604
AMP
9
T1D
2
community
Genome assembly (visualization)
486
hg19
422
GRCh38
Lab
568
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
92
inconsistent ontology term
1
inconsistent replicate
Audit category:
7
missing controlled_by
Audit category:
15
inconsistent control read length
1
inconsistent assembly
month_released!
January, 2019
target.investigated_as!
chromatin remodeller
BIOSAMPLE
ASSAY
615 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
358
9
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
38
1
Panc1
13
1
1
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