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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
465
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
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
465
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
38
histone
38
histone modification
30
chromatin remodeller
19
broad histone mark
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
308
November, 2017
61
November, 2018
28
December, 2018
25
August, 2021
23
October, 2019
18
February, 2021
17
January, 2019
16
May, 2021
11
November, 2019
6
November, 2020
4
February, 2023
2
March, 2023
1
January, 2018
1
March, 2020
1
October, 2022
Available data
565
bam
503
bigWig
419
fastq
386
bed narrowPeak
345
bigBed narrowPeak
tsv
53
bed broadPeak
53
bigBed broadPeak
15
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
518
Homo sapiens
Biosample type
1377
tissue
703
primary cell
522
cell line
208
in vitro differentiated cells
5
stem cell
Organ
377
liver
60
blood
60
bodily fluid
49
pancreas
38
epithelium
14
artery
14
blood vessel
14
heart
14
vasculature
13
kidney
Project
517
AMP
3
T1D
2
community
Genome assembly (visualization)
406
hg19
344
GRCh38
Lab
488
AMP-T2D consortium
23
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
3
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
47
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
12
missing controlled_by
Audit category:
21
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_title!
HiChIP
target.investigated_as!
narrow histone mark
files.file_type!
tsv
BIOSAMPLE
ASSAY
522 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
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
pCHi-C
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
369
1
2
2
1
1
1
GM12878
59
1
EndoC_BH1
9
18
6
1
3
2
1
smooth muscle cell of the coronary artery
6
8
Panc1
10
1
1
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