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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
387
ChIP-seq
108
total RNA-seq
28
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
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
1
whole genome sequencing assay
Assay category
387
DNA binding
110
Transcription
30
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
310
transcription factor
89
recombinant protein
77
control
55
RNA binding protein
histone
37
histone modification
20
chromatin remodeller
19
broad histone mark
18
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
300
November, 2017
96
February, 2021
46
November, 2018
41
August, 2021
23
October, 2019
20
May, 2021
10
March, 2020
6
February, 2023
6
November, 2019
6
November, 2020
January, 2019
2
March, 2023
1
December, 2018
1
May, 2020
1
October, 2022
Available data
483
bam
426
bigWig
347
fastq
316
bed narrowPeak
282
bigBed narrowPeak
114
tsv
45
bed broadPeak
45
bigBed broadPeak
9
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
555
Homo sapiens
Biosample type
2147
tissue
843
primary cell
559
cell line
282
in vitro differentiated cells
8
stem cell
Organ
378
liver
73
pancreas
67
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
43
blood
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
550
AMP
7
T1D
2
community
Genome assembly (visualization)
434
hg19
374
GRCh38
Lab
515
AMP-T2D consortium
31
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
80
inconsistent ontology term
1
inconsistent replicate
Audit category:
12
missing controlled_by
Audit category:
15
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
month_released!
January, 2019
organ_slims!
bodily fluid
intestine
target.investigated_as!
histone
BIOSAMPLE
ASSAY
559 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
360
9
1
2
2
2
1
1
EndoC_BH1
3
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
H1-hESC
8
Panc1
6
1
1
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