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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
436
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
436
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
65
RNA binding protein
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
300
November, 2017
96
February, 2021
61
November, 2018
39
August, 2021
28
December, 2018
22
January, 2019
20
May, 2021
8
March, 2020
8
October, 2019
6
February, 2023
6
November, 2019
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
532
bam
473
bigWig
411
fastq
361
bed narrowPeak
334
bigBed narrowPeak
113
tsv
45
bed broadPeak
45
bigBed broadPeak
9
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
601
Homo sapiens
Biosample type
1866
tissue
825
primary cell
605
cell line
282
in vitro differentiated cells
8
stem cell
Organ
383
liver
73
pancreas
67
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
60
blood
60
bodily fluid
kidney
8
embryo
1
mammary gland
Project
596
AMP
7
T1D
2
community
Genome assembly (visualization)
481
hg19
420
GRCh38
Lab
563
AMP-T2D consortium
29
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
65
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
12
missing controlled_by
Audit category:
15
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
organ_slims!
kidney
target.investigated_as!
histone
BIOSAMPLE
ASSAY
605 results
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Clear Filters
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
360
14
1
2
2
2
1
1
EndoC_BH1
3
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
59
1
H1-hESC
8
Panc1
6
1
1
EndoC-BH1
1
1
early embryonic cell
2
iPSC derived cell line
2
MCF-7
1
MIN6
1
Synthesized DNA
1
fibroblast cell line
1
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