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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
448
ChIP-seq
99
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
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
Assay category
448
DNA binding
101
Transcription
31
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
336
transcription factor
89
recombinant protein
76
control
58
RNA binding protein
34
histone
34
histone modification
24
chromatin remodeller
18
broad histone mark
16
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
96
February, 2021
61
November, 2018
30
October, 2019
28
December, 2018
January, 2019
21
May, 2021
16
November, 2019
11
March, 2020
10
August, 2021
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
559
bam
488
bigWig
404
fastq
375
bed narrowPeak
340
bigBed narrowPeak
105
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
1
hic
1
txt
Organism
601
Homo sapiens
Biosample type
2726
tissue
1088
primary cell
605
cell line
394
in vitro differentiated cells
10
stem cell
Organ
365
liver
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
43
blood
43
bodily fluid
17
kidney
8
embryo
1
mammary gland
Project
594
AMP
9
T1D
2
community
Genome assembly (visualization)
495
hg19
444
GRCh38
Lab
592
AMP-T2D consortium
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
91
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
month_released!
January, 2019
lab.title!
Bing Ren, UCSD
BIOSAMPLE
ASSAY
605 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
360
1
2
1
1
EndoC_BH1
15
33
19
6
3
1
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
42
1
Panc1
13
1
1
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