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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
146
ChIP-seq
113
total RNA-seq
29
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
146
DNA binding
115
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
120
transcription factor
31
RNA binding protein
27
control
histone
23
histone modification
23
recombinant protein
15
chromatin remodeller
12
narrow histone mark
11
broad histone mark
3
nucleotide modification
Date released
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
6
November, 2019
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
248
bam
232
bigWig
133
bed narrowPeak
119
tsv
111
fastq
99
bigBed narrowPeak
8
tagAlign
3
bed bed3+
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bed broadPeak
1
bigBed bedMethyl
1
bigBed broadPeak
1
hdf5
1
txt
1
vcf
Organism
320
Homo sapiens
Biosample type
2133
tissue
845
primary cell
324
cell line
282
in vitro differentiated cells
8
stem cell
Organ
83
liver
73
pancreas
67
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
60
blood
60
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
315
AMP
7
T1D
2
community
Genome assembly (visualization)
242
hg19
228
GRCh38
Lab
280
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 control
1
inconsistent replicate
Audit category:
3
missing controlled_by
Audit category:
5
inconsistent control read length
4
inconsistent control run_type
1
inconsistent assembly
target.investigated_as!
histone
month_released!
November, 2017
BIOSAMPLE
ASSAY
324 results
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Clear Filters
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
60
14
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
GM12878
59
1
H1-hESC
8
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