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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
639
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
3
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
639
DNA binding
253
Transcription
74
DNA accessibility
8
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
385
transcription factor
132
histone
132
histone modification
120
control
88
recombinant protein
70
RNA binding protein
67
narrow histone mark
64
broad histone mark
20
chromatin remodeller
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
294
November, 2017
153
May, 2021
122
February, 2021
86
August, 2021
62
August, 2017
56
November, 2018
38
October, 2019
37
February, 2018
34
December, 2017
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
830
bam
738
bigWig
525
fastq
495
bed narrowPeak
348
bigBed narrowPeak
250
tsv
49
tagAlign
47
bed broadPeak
47
bigBed broadPeak
20
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
1009
Homo sapiens
Biosample type
2731
tissue
1083
primary cell
636
cell line
377
in vitro differentiated cells
8
stem cell
Organ
390
liver
102
epithelium
95
pancreas
91
connective tissue
67
heart
66
artery
66
blood vessel
66
vasculature
61
blood
61
bodily fluid
34
embryo
19
kidney
1
adipose tissue
1
mammary gland
Project
1002
AMP
9
T1D
2
community
Genome assembly (visualization)
784
hg19
690
GRCh38
4
hg18
Lab
912
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:
206
inconsistent ontology term
2
audit script error
1
inconsistent control
1
inconsistent replicate
Audit category:
14
missing controlled_by
Audit category:
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
audit.WARNING.category!
inconsistent control read length
BIOSAMPLE
ASSAY
1013 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
352
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
adipocyte
61
5
8
1
1
cardiomyocytes
3
59
embryonic stem cell
40
7
6
1
neural progenitor cell
21
7
10
cardiac precursors (cardiac muscle cell)
19
1
1
+ See 31 more…
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