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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
615
ChIP-seq
249
total RNA-seq
71
ATAC-seq
11
pCHi-C
8
Hi-C
6
MeRIP-seq
5
STARR-seq
4
Capture-C
4
GRO-seq
3
CRISPR genome editing followed by DNA sequencing
2
DNase-seq
2
HiChIP
2
single cell RNA-seq
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
615
DNA binding
253
Transcription
73
DNA accessibility
8
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
388
transcription factor
113
histone
113
histone modification
112
control
89
recombinant protein
72
RNA binding protein
58
narrow histone mark
55
broad histone mark
31
chromatin remodeller
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
153
May, 2021
122
February, 2021
86
August, 2021
August, 2017
61
November, 2018
43
December, 2017
39
February, 2018
38
October, 2019
28
December, 2018
23
January, 2019
22
February, 2023
21
November, 2019
19
March, 2020
6
November, 2020
5
January, 2018
2
December, 2019
2
March, 2023
1
August, 2018
1
May, 2020
1
October, 2022
Available data
819
bam
733
bigWig
514
fastq
493
bed narrowPeak
371
bigBed narrowPeak
250
tsv
59
bed broadPeak
59
bigBed broadPeak
46
tagAlign
21
bed bed3+
9
bedpe bed3+
7
bed bedgraph
6
bed bed3
6
hic
4
txt
3
tar
2
ibed
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
vcf
Organism
984
Homo sapiens
Biosample type
2453
tissue
1029
primary cell
662
cell line
326
in vitro differentiated cells
10
stem cell
Organ
416
liver
103
epithelium
95
pancreas
67
heart
66
artery
66
blood vessel
66
vasculature
61
blood
61
bodily fluid
37
embryo
29
connective tissue
19
kidney
1
adipose tissue
1
mammary gland
Project
977
AMP
9
T1D
2
community
Genome assembly (visualization)
778
hg19
680
GRCh38
4
hg18
Lab
887
AMP-T2D consortium
52
Kyle Gaulton, UCSD
34
Bing Ren, UCSD
7
Struan F.A. Grant, CHOP
6
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
Audit category:
207
inconsistent ontology term
2
audit script error
1
inconsistent control
1
inconsistent replicate
Audit category:
14
missing controlled_by
Audit category:
37
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
month_released!
August, 2017
BIOSAMPLE
ASSAY
988 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
Hi-C
MeRIP-seq
STARR-seq
Capture-C
GRO-seq
CRISPR genome editing followed by DNA sequencing
DNase-seq
HiChIP
single cell RNA-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
1
6
2
3
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
+ See 14 more…
in vitro differentiated cells
cardiomyocytes
3
59
embryonic stem cell
40
7
6
1
neural progenitor cell
21
7
10
pancreatic endoderm
18
4
1
cardiac precursors (cardiac muscle cell)
19
1
1
+ See 31 more…
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