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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
404
ChIP-seq
105
total RNA-seq
29
ATAC-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
MeRIP-seq
2
Capture-C
2
DNase-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
404
DNA binding
107
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
89
recombinant protein
control
65
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
259
November, 2017
93
February, 2021
58
November, 2018
32
August, 2021
28
December, 2018
21
May, 2021
21
October, 2019
20
January, 2019
14
November, 2019
11
March, 2020
3
November, 2020
2
March, 2023
1
February, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
501
bigWig
498
bam
404
bed narrowPeak
365
fastq
355
bigBed narrowPeak
111
tsv
59
bed broadPeak
59
bigBed broadPeak
16
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
562
Homo sapiens
Biosample type
2538
tissue
817
primary cell
566
cell line
293
in vitro differentiated cells
9
stem cell
Organ
341
liver
81
pancreas
74
epithelium
64
artery
64
blood vessel
64
heart
64
vasculature
55
blood
55
bodily fluid
16
kidney
embryo
1
mammary gland
Project
560
AMP
4
T1D
2
community
Genome assembly (visualization)
509
hg19
456
GRCh38
Lab
531
AMP-T2D consortium
30
Bing Ren, UCSD
Kyle Gaulton, UCSD
3
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
Audit category:
84
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
lab.title!
Kyle Gaulton, UCSD
organ_slims!
embryo
target.investigated_as!
control
BIOSAMPLE
ASSAY
566 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
STARR-seq
Hi-C
MeRIP-seq
Capture-C
DNase-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
318
14
1
2
2
2
1
1
EndoC_BH1
13
33
19
1
3
2
1
smooth muscle cell of the coronary artery
4
52
8
GM12878
54
1
Panc1
7
1
1
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