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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
382
ChIP-seq
112
total RNA-seq
28
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
2
Hi-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
382
DNA binding
114
Transcription
30
DNA accessibility
2
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
360
transcription factor
recombinant protein
81
control
64
RNA binding protein
30
chromatin remodeller
28
histone
28
histone modification
15
narrow histone mark
13
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
249
November, 2017
96
February, 2021
45
November, 2018
43
August, 2021
28
December, 2018
23
January, 2019
23
October, 2019
21
May, 2021
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
478
bam
422
bigWig
345
fastq
304
bed narrowPeak
274
bigBed narrowPeak
118
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
hic
1
txt
1
vcf
Organism
552
Homo sapiens
Biosample type
2727
tissue
1082
primary cell
556
cell line
385
in vitro differentiated cells
10
stem cell
Organ
318
liver
76
pancreas
66
artery
66
blood vessel
66
heart
66
vasculature
63
epithelium
61
blood
61
bodily fluid
12
kidney
8
embryo
1
mammary gland
Project
545
AMP
9
T1D
2
community
Genome assembly (visualization)
430
hg19
363
GRCh38
Lab
510
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:
69
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
12
missing controlled_by
Audit category:
25
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
files.file_type!
hic
month_released!
November, 2019
target.investigated_as!
recombinant protein
BIOSAMPLE
ASSAY
556 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
Hi-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
296
14
1
2
2
1
1
1
EndoC_BH1
2
32
18
6
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
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