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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
484
ChIP-seq
28
ATAC-seq
6
MeRIP-seq
5
STARR-seq
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
484
DNA binding
30
DNA accessibility
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
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
November, 2018
27
December, 2018
26
August, 2021
25
October, 2019
18
February, 2021
18
January, 2019
17
May, 2021
14
November, 2019
6
February, 2023
6
November, 2020
2
March, 2020
2
March, 2023
1
January, 2018
1
October, 2022
Available data
574
bam
513
bigWig
426
fastq
404
bed narrowPeak
355
bigBed narrowPeak
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
tar
2
bed bed3+
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
txt
1
vcf
Organism
535
Homo sapiens
Biosample type
1685
tissue
808
primary cell
539
cell line
236
in vitro differentiated cells
6
stem cell
Organ
384
liver
61
blood
61
bodily fluid
56
pancreas
43
epithelium
14
artery
14
blood vessel
14
heart
14
vasculature
13
kidney
Project
530
AMP
7
T1D
2
community
Genome assembly (visualization)
422
hg19
359
GRCh38
Lab
502
AMP-T2D consortium
24
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
52
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
organ_slims!
embryo
files.file_type!
tsv
assay_slims!
3D chromatin structure
BIOSAMPLE
ASSAY
539 results
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ChIP-seq
ATAC-seq
MeRIP-seq
STARR-seq
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
378
1
2
1
1
1
GM12878
60
1
EndoC_BH1
15
18
6
3
2
2
1
Panc1
13
1
smooth muscle cell of the coronary artery
6
8
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