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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
409
ChIP-seq
109
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
3
STARR-seq
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
409
DNA binding
111
Transcription
30
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
329
transcription factor
82
recombinant protein
80
control
63
RNA binding protein
38
histone
histone modification
28
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
300
November, 2017
96
February, 2021
61
November, 2018
39
August, 2021
December, 2018
22
January, 2019
20
May, 2021
8
March, 2020
8
October, 2019
6
February, 2023
6
November, 2019
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
505
bam
446
bigWig
383
fastq
334
bed narrowPeak
307
bigBed narrowPeak
113
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
573
Homo sapiens
Biosample type
1863
tissue
825
primary cell
577
cell line
282
in vitro differentiated cells
8
stem cell
Organ
382
liver
73
pancreas
67
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
33
blood
33
bodily fluid
kidney
8
embryo
1
mammary gland
Project
568
AMP
7
T1D
2
community
Genome assembly (visualization)
454
hg19
393
GRCh38
Lab
535
AMP-T2D consortium
29
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
65
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
target.investigated_as!
histone modification
month_released!
December, 2018
organ_slims!
kidney
BIOSAMPLE
ASSAY
577 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
STARR-seq
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
360
14
1
2
1
2
1
1
EndoC_BH1
3
33
19
6
3
1
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
32
1
H1-hESC
8
Panc1
6
1
1
EndoC-BH1
1
1
early embryonic cell
2
iPSC derived cell line
2
MCF-7
1
MIN6
1
Synthesized DNA
1
fibroblast cell line
1
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