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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
406
ChIP-seq
104
total RNA-seq
28
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
WGBS
Assay category
406
DNA binding
104
Transcription
30
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
299
transcription factor
89
recombinant protein
73
control
54
RNA binding protein
34
histone
34
histone modification
20
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
46
November, 2018
30
October, 2019
21
May, 2021
16
November, 2019
11
March, 2020
10
August, 2021
6
November, 2020
5
February, 2023
5
January, 2019
1
December, 2018
1
May, 2020
Available data
522
bam
453
bigWig
367
fastq
336
bed narrowPeak
301
bigBed narrowPeak
110
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
Organism
563
Homo sapiens
Biosample type
2764
tissue
1080
primary cell
563
cell line
394
in vitro differentiated cells
8
stem cell
Organ
370
liver
91
pancreas
78
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
bodily fluid
17
kidney
8
embryo
1
mammary gland
Project
554
AMP
9
T1D
Genome assembly (visualization)
460
hg19
410
GRCh38
Lab
552
AMP-T2D consortium
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
Audit category:
91
inconsistent ontology term
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!
Bing Ren, UCSD
organ_slims!
bodily fluid
BIOSAMPLE
ASSAY
563 results
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Clear Filters
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
WGBS
cell line
HepG2
360
5
1
2
1
1
EndoC_BH1
15
33
19
6
3
1
2
2
smooth muscle cell of the coronary artery
6
52
8
Panc1
13
1
1
H1-hESC
8
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