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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
380
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
3
Hi-C
2
Capture-C
2
DNase-seq
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
whole genome sequencing assay
Assay category
380
DNA binding
112
Transcription
30
DNA accessibility
3
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
other context
2
other post-translational modification
Date released
247
November, 2017
96
February, 2021
45
November, 2018
44
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
1
January, 2018
1
May, 2020
1
October, 2022
Available data
476
bam
420
bigWig
343
fastq
302
bed narrowPeak
272
bigBed narrowPeak
118
tsv
58
bed broadPeak
58
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
1
vcf
Organism
551
Homo sapiens
Biosample type
2734
tissue
1088
primary cell
553
cell line
389
in vitro differentiated cells
8
stem cell
Organ
317
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
544
AMP
9
T1D
community
Genome assembly (visualization)
429
hg19
361
GRCh38
Lab
508
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
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
award.project!
community
month_released!
November, 2019
target.investigated_as!
other context
recombinant protein
BIOSAMPLE
ASSAY
553 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
Hi-C
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
whole genome sequencing assay
cell line
HepG2
294
14
1
2
2
2
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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