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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
384
ChIP-seq
77
total RNA-seq
10
ATAC-seq
4
STARR-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
DNase-seq
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
384
DNA binding
79
Transcription
12
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
353
transcription factor
82
recombinant protein
control
64
RNA binding protein
30
chromatin remodeller
26
histone
26
histone modification
13
broad histone mark
13
narrow histone mark
2
other context
2
other post-translational modification
Date released
259
November, 2017
67
February, 2021
58
November, 2018
37
August, 2021
28
December, 2018
20
January, 2019
11
October, 2019
6
February, 2023
4
March, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
451
bigWig
449
bam
383
bed narrowPeak
365
fastq
355
bigBed narrowPeak
80
tsv
59
bed broadPeak
59
bigBed broadPeak
16
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
1
vcf
Organism
491
Homo sapiens
Biosample type
2459
tissue
1004
primary cell
495
cell line
244
in vitro differentiated cells
8
stem cell
Organ
341
liver
64
artery
64
blood vessel
64
heart
64
vasculature
55
blood
55
bodily fluid
10
pancreas
8
embryo
4
kidney
3
epithelium
1
mammary gland
Project
488
AMP
5
T1D
2
community
Genome assembly (visualization)
457
hg19
407
GRCh38
Lab
459
AMP-T2D consortium
29
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
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
audit.ERROR.category!
inconsistent ontology term
target.investigated_as!
control
BIOSAMPLE
ASSAY
495 results
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ChIP-seq
total RNA-seq
ATAC-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
318
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
4
52
8
GM12878
54
1
Panc1
7
1
1
H1-hESC
8
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