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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
443
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
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
443
DNA binding
114
Transcription
30
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
360
transcription factor
89
recombinant protein
81
control
64
RNA binding protein
30
chromatin remodeller
histone
28
histone modification
15
narrow histone mark
13
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
300
November, 2017
96
February, 2021
61
November, 2018
41
August, 2021
28
December, 2018
23
October, 2019
22
January, 2019
20
May, 2021
10
March, 2020
6
February, 2023
November, 2019
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
542
bam
483
bigWig
411
fastq
367
bed narrowPeak
335
bigBed narrowPeak
118
tsv
45
bed broadPeak
45
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
1
vcf
Organism
614
Homo sapiens
Biosample type
2109
tissue
851
primary cell
618
cell line
277
in vitro differentiated cells
8
stem cell
Organ
383
liver
67
pancreas
66
artery
66
blood vessel
66
heart
66
vasculature
61
epithelium
60
blood
60
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
609
AMP
7
T1D
2
community
Genome assembly (visualization)
489
hg19
429
GRCh38
Lab
574
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:
74
inconsistent ontology term
1
inconsistent control
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!
November, 2019
August, 2022
target.investigated_as!
histone
BIOSAMPLE
ASSAY
618 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
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
360
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
EndoC_BH1
32
18
6
3
2
2
1
GM12878
59
1
H1-hESC
8
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