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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
446
ChIP-seq
28
ATAC-seq
6
MeRIP-seq
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
pCHi-C
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
446
DNA binding
30
DNA accessibility
4
3D chromatin structure
2
Transcription
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
89
recombinant protein
83
control
65
RNA binding protein
histone
38
histone modification
30
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
61
November, 2018
28
December, 2018
24
August, 2021
19
October, 2019
18
February, 2021
17
January, 2019
16
May, 2021
6
February, 2023
6
November, 2020
5
November, 2019
2
March, 2023
1
January, 2018
1
March, 2020
1
October, 2022
Available data
547
bam
485
bigWig
411
fastq
369
bed narrowPeak
335
bigBed narrowPeak
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
501
Homo sapiens
Biosample type
1069
tissue
581
primary cell
505
cell line
151
in vitro differentiated cells
4
stem cell
Organ
368
liver
60
blood
60
bodily fluid
39
pancreas
32
epithelium
14
artery
14
blood vessel
14
heart
14
vasculature
13
kidney
Project
498
AMP
5
T1D
2
community
Genome assembly (visualization)
388
hg19
328
GRCh38
Lab
470
AMP-T2D consortium
22
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
41
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
target.investigated_as!
histone
files.file_type!
tsv
BIOSAMPLE
ASSAY
505 results
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Clear Filters
ChIP-seq
ATAC-seq
MeRIP-seq
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
pCHi-C
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
360
1
2
2
1
1
1
GM12878
59
1
EndoC_BH1
3
18
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
8
Panc1
6
1
1
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