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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
440
ChIP-seq
104
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
440
DNA binding
106
Transcription
31
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
335
transcription factor
88
recombinant protein
79
control
58
RNA binding protein
24
histone
24
histone modification
19
chromatin remodeller
12
broad histone mark
12
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
294
November, 2017
96
February, 2021
56
November, 2018
30
October, 2019
28
December, 2018
23
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
556
bam
482
bigWig
401
fastq
366
bed narrowPeak
331
bigBed narrowPeak
110
tsv
46
bed broadPeak
46
bigBed broadPeak
9
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
598
Homo sapiens
Biosample type
2766
tissue
1083
primary cell
602
cell line
377
in vitro differentiated cells
8
stem cell
Organ
344
liver
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
17
kidney
8
embryo
1
mammary gland
Project
591
AMP
9
T1D
2
community
Genome assembly (visualization)
489
hg19
442
GRCh38
Lab
589
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:
8
missing controlled_by
Audit category:
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
lab.title!
Bing Ren, UCSD
Maike Sander, UCSD
audit.WARNING.category!
inconsistent control read length
BIOSAMPLE
ASSAY
602 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
334
5
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
60
1
Panc1
13
1
1
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