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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
680
ChIP-seq
247
total RNA-seq
66
ATAC-seq
11
pCHi-C
8
Hi-C
6
MeRIP-seq
5
STARR-seq
4
GRO-seq
3
DNase-seq
2
Capture-C
2
single cell RNA-seq
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
680
DNA binding
251
Transcription
69
DNA accessibility
8
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
410
transcription factor
148
histone
148
histone modification
120
control
89
recombinant protein
76
RNA binding protein
75
broad histone mark
72
narrow histone mark
33
chromatin remodeller
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
152
May, 2021
122
February, 2021
82
August, 2021
68
August, 2017
61
November, 2018
43
December, 2017
39
February, 2018
38
October, 2019
28
December, 2018
23
January, 2019
21
November, 2019
16
March, 2020
14
February, 2023
6
November, 2020
5
January, 2018
2
December, 2019
2
March, 2023
1
August, 2018
1
May, 2020
1
October, 2022
Available data
869
bam
772
bigWig
568
fastq
530
bed narrowPeak
372
bigBed narrowPeak
248
tsv
60
bed broadPeak
60
bigBed broadPeak
60
tagAlign
26
bed bed3+
9
bedpe bed3+
6
bed bed3
6
hic
4
bed bedgraph
3
tar
2
ibed
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
1036
Homo sapiens
Biosample type
2746
tissue
884
primary cell
653
cell line
387
in vitro differentiated cells
10
stem cell
Organ
416
liver
99
epithelium
93
connective tissue
91
pancreas
67
heart
66
artery
66
blood vessel
66
vasculature
61
blood
61
bodily fluid
37
embryo
19
kidney
1
adipose tissue
1
mammary gland
Project
1038
AMP
T1D
2
community
Genome assembly (visualization)
816
hg19
725
GRCh38
4
hg18
Lab
951
AMP-T2D consortium
47
Kyle Gaulton, UCSD
34
Bing Ren, UCSD
Struan F.A. Grant, CHOP
6
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
Audit category:
202
inconsistent ontology term
2
audit script error
1
inconsistent control
1
inconsistent replicate
Audit category:
19
missing controlled_by
Audit category:
43
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
award.project!
T1D
lab.title!
Struan F.A. Grant, CHOP
BIOSAMPLE
ASSAY
1040 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
Hi-C
MeRIP-seq
STARR-seq
GRO-seq
DNase-seq
Capture-C
single cell RNA-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
14
1
2
2
2
1
1
EndoC_BH1
13
31
19
1
6
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
+ See 14 more…
in vitro differentiated cells
adipocyte
67
5
7
1
cardiomyocytes
3
59
embryonic stem cell
40
7
5
1
neural progenitor cell
21
7
10
pancreatic endoderm
18
4
1
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