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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
447
ChIP-seq
108
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
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
447
DNA binding
110
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
347
transcription factor
89
recombinant protein
80
control
59
RNA binding protein
37
histone
37
histone modification
24
chromatin remodeller
broad histone mark
18
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
307
November, 2017
96
February, 2021
61
November, 2018
43
August, 2021
28
December, 2018
26
October, 2019
January, 2019
21
May, 2021
11
March, 2020
10
November, 2019
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
541
bam
484
bigWig
396
fastq
372
bed narrowPeak
330
bigBed narrowPeak
114
tsv
51
bed broadPeak
51
bigBed broadPeak
14
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
616
Homo sapiens
Biosample type
2471
tissue
966
primary cell
620
cell line
338
in vitro differentiated cells
9
stem cell
Organ
387
liver
82
pancreas
73
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
43
blood
43
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
609
AMP
9
T1D
2
community
Genome assembly (visualization)
492
hg19
428
GRCh38
Lab
574
AMP-T2D consortium
33
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
86
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
20
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
month_released!
January, 2019
target.investigated_as!
broad histone mark
BIOSAMPLE
ASSAY
620 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
369
9
1
2
2
2
1
1
EndoC_BH1
9
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
42
1
Panc1
9
1
1
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