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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
409
ChIP-seq
109
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
4
Hi-C
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
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
409
DNA binding
111
Transcription
30
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
354
transcription factor
82
recombinant protein
80
control
RNA binding protein
38
histone
38
histone modification
30
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
281
November, 2017
96
February, 2021
41
August, 2021
40
November, 2018
26
December, 2018
21
May, 2021
17
January, 2019
15
November, 2019
15
October, 2019
9
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
503
bam
447
bigWig
364
fastq
333
bed narrowPeak
293
bigBed narrowPeak
113
tsv
55
bed broadPeak
55
bigBed broadPeak
20
tagAlign
3
bed bed3+
2
bedpe bed3+
2
hic
2
tar
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
574
Homo sapiens
Biosample type
2416
tissue
1044
primary cell
578
cell line
383
in vitro differentiated cells
10
stem cell
Organ
347
liver
91
pancreas
78
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
51
blood
51
bodily fluid
kidney
8
embryo
1
mammary gland
Project
567
AMP
9
T1D
2
community
Genome assembly (visualization)
456
hg19
394
GRCh38
Lab
534
AMP-T2D consortium
31
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
76
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
11
missing controlled_by
Audit category:
20
inconsistent control read length
5
inconsistent control run_type
1
inconsistent assembly
organ_slims!
kidney
target.investigated_as!
RNA binding protein
BIOSAMPLE
ASSAY
578 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
Hi-C
pCHi-C
CRISPR genome editing followed by DNA sequencing
STARR-seq
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
324
14
1
2
2
2
1
1
EndoC_BH1
14
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
50
1
Panc1
13
1
1
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