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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
434
ChIP-seq
113
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
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
whole genome sequencing assay
Assay category
434
DNA binding
113
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
349
transcription factor
88
recombinant protein
83
control
63
RNA binding protein
37
histone
histone modification
24
chromatin remodeller
19
broad histone mark
18
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
291
November, 2017
96
February, 2021
58
November, 2018
41
August, 2021
28
December, 2018
23
October, 2019
22
January, 2019
20
May, 2021
10
March, 2020
6
February, 2023
6
November, 2019
6
November, 2020
1
January, 2018
1
May, 2020
1
October, 2022
Available data
535
bam
474
bigWig
399
fastq
358
bed narrowPeak
324
bigBed narrowPeak
119
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
608
Homo sapiens
Biosample type
2131
tissue
851
primary cell
610
cell line
277
in vitro differentiated cells
6
stem cell
Organ
371
liver
73
pancreas
67
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
60
blood
60
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
603
AMP
7
T1D
community
Genome assembly (visualization)
482
hg19
428
GRCh38
Lab
568
AMP-T2D consortium
31
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
Audit category:
80
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
missing controlled_by
Audit category:
10
inconsistent control read length
2
inconsistent control run_type
1
inconsistent assembly
target.investigated_as!
histone modification
award.project!
community
audit.NOT_COMPLIANT.category!
missing controlled_by
BIOSAMPLE
ASSAY
610 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
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
whole genome sequencing assay
cell line
HepG2
348
14
1
2
2
2
1
1
EndoC_BH1
3
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
59
1
H1-hESC
8
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