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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
448
ChIP-seq
109
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
4
Hi-C
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
STARR-seq
2
Capture-C
2
HiChIP
1
DNase-seq
1
WGBS
1
whole genome sequencing assay
Assay category
448
DNA binding
109
Transcription
30
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
339
transcription factor
81
recombinant protein
80
control
59
RNA binding protein
27
histone
27
histone modification
19
chromatin remodeller
14
narrow histone mark
13
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
294
November, 2017
96
February, 2021
56
November, 2018
42
August, 2021
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
15
October, 2019
9
March, 2020
6
November, 2020
5
February, 2023
1
January, 2018
1
May, 2020
Available data
541
bam
484
bigWig
401
fastq
372
bed narrowPeak
330
bigBed narrowPeak
113
tsv
46
bed broadPeak
46
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
vcf
Organism
613
Homo sapiens
Biosample type
2463
tissue
1047
primary cell
613
cell line
377
in vitro differentiated cells
6
stem cell
Organ
375
liver
91
pancreas
78
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
kidney
8
embryo
1
mammary gland
Project
604
AMP
9
T1D
Genome assembly (visualization)
492
hg19
430
GRCh38
Lab
570
AMP-T2D consortium
32
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
Audit category:
77
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
8
missing controlled_by
Audit category:
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
audit.WARNING.category!
inconsistent control read length
organ_slims!
kidney
BIOSAMPLE
ASSAY
613 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
Hi-C
pCHi-C
CRISPR genome editing followed by DNA sequencing
STARR-seq
Capture-C
HiChIP
DNase-seq
WGBS
whole genome sequencing assay
cell line
HepG2
352
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
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