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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
472
ChIP-seq
107
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
4
Hi-C
4
pCHi-C
3
STARR-seq
2
Capture-C
1
CRISPR genome editing followed by sgRNA sequencing
1
DNase-seq
1
MPRA
1
WGBS
1
whole genome sequencing assay
Assay category
472
DNA binding
107
Transcription
30
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
354
transcription factor
82
recombinant protein
80
control
65
RNA binding protein
36
histone
36
histone modification
30
chromatin remodeller
19
broad histone mark
17
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
96
February, 2021
61
November, 2018
42
August, 2021
28
December, 2018
23
January, 2019
20
May, 2021
16
November, 2019
15
October, 2019
6
March, 2020
6
November, 2020
1
February, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
563
bam
506
bigWig
427
fastq
394
bed narrowPeak
354
bigBed narrowPeak
111
tsv
59
bed broadPeak
59
bigBed broadPeak
20
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
630
Homo sapiens
Biosample type
2388
tissue
632
cell line
523
primary cell
394
in vitro differentiated cells
8
stem cell
Organ
401
liver
88
pancreas
75
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
kidney
8
embryo
1
mammary gland
Project
632
AMP
9
T1D
2
community
Genome assembly (visualization)
514
hg19
448
GRCh38
Lab
594
AMP-T2D consortium
32
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
Audit category:
73
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
1
inconsistent assembly
organ_slims!
kidney
BIOSAMPLE
ASSAY
632 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
Hi-C
pCHi-C
STARR-seq
Capture-C
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
MPRA
WGBS
whole genome sequencing assay
cell line
HepG2
378
14
1
2
2
2
1
1
EndoC_BH1
13
31
19
6
1
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
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