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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
416
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
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
416
DNA binding
111
Transcription
29
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
310
transcription factor
82
recombinant protein
80
control
61
RNA binding protein
26
chromatin remodeller
24
histone
24
histone modification
13
narrow histone mark
11
broad histone mark
3
nucleotide modification
1
other context
1
other post-translational modification
Date released
257
November, 2017
96
February, 2021
61
November, 2018
42
August, 2021
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
14
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
567
bam
510
bigWig
427
fastq
396
bed narrowPeak
354
bigBed narrowPeak
113
tsv
59
bed broadPeak
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
580
Homo sapiens
Biosample type
2330
tissue
1013
primary cell
584
cell line
393
in vitro differentiated cells
10
stem cell
Organ
343
liver
91
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
kidney
8
embryo
1
mammary gland
Project
573
AMP
9
T1D
2
community
Genome assembly (visualization)
459
hg19
407
GRCh38
Lab
539
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:
77
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
13
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
files.file_type!
bigBed broadPeak
organ_slims!
kidney
BIOSAMPLE
ASSAY
584 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
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
320
14
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
60
1
Panc1
13
1
H1-hESC
8
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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