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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
521
ChIP-seq
124
total RNA-seq
41
ATAC-seq
6
pCHi-C
4
GRO-seq
4
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
DNase-seq
3
Hi-C
2
Capture-C
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
521
DNA binding
126
Transcription
44
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
348
transcription factor
135
histone
135
histone modification
104
control
82
recombinant protein
broad histone mark
65
RNA binding protein
65
narrow histone mark
23
chromatin remodeller
2
other context
2
other post-translational modification
Date released
307
November, 2017
78
February, 2021
75
August, 2021
54
May, 2021
48
August, 2017
46
November, 2018
31
February, 2018
28
December, 2017
17
February, 2023
15
October, 2019
5
January, 2019
5
March, 2020
4
January, 2018
2
March, 2023
1
August, 2018
1
December, 2018
1
May, 2020
1
October, 2022
Available data
601
bam
526
bigWig
465
fastq
400
bed narrowPeak
301
bigBed narrowPeak
121
tsv
52
bed broadPeak
52
bigBed broadPeak
37
tagAlign
22
bed bed3+
6
bed bed3
6
bed bedgraph
3
tar
3
txt
2
bedpe bed3+
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
hic
1
vcf
Organism
715
Homo sapiens
Biosample type
2383
tissue
912
primary cell
496
cell line
223
in vitro differentiated cells
8
stem cell
Organ
400
liver
73
connective tissue
67
heart
66
artery
66
blood vessel
66
vasculature
61
blood
bodily fluid
27
embryo
15
epithelium
15
pancreas
4
kidney
1
adipose tissue
1
mammary gland
Project
712
AMP
5
T1D
2
community
Genome assembly (visualization)
556
hg19
472
GRCh38
4
hg18
Lab
637
AMP-T2D consortium
42
Kyle Gaulton, UCSD
32
Bing Ren, UCSD
6
Struan F.A. Grant, CHOP
2
Anna Gloyn, Oxford
Audit category:
inconsistent ontology term
2
audit script error
1
inconsistent replicate
Audit category:
19
missing controlled_by
Audit category:
31
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
audit.ERROR.category!
inconsistent ontology term
organ_slims!
bodily fluid
target.investigated_as!
broad histone mark
BIOSAMPLE
ASSAY
719 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
GRO-seq
STARR-seq
CRISPR genome editing followed by DNA sequencing
DNase-seq
Hi-C
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
369
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
Panc1
9
1
1
H1-hESC
8
EndoC_BH1
3
2
1
+ See 8 more…
in vitro differentiated cells
adipocyte
47
5
8
1
1
embryonic stem cell
29
7
6
1
neural progenitor cell
14
7
10
pancreatic endoderm
14
4
1
definitive endodermal cell
6
2
1
+ See 18 more…
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