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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
611
ChIP-seq
100
total RNA-seq
30
ATAC-seq
6
pCHi-C
4
GRO-seq
3
CRISPR genome editing followed by DNA sequencing
3
DNase-seq
2
Hi-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
Assay category
611
DNA binding
102
Transcription
33
DNA accessibility
2
3D chromatin structure
1
DNA methylation
Target of assay
388
transcription factor
119
histone
119
histone modification
99
control
82
recombinant protein
74
RNA binding protein
61
broad histone mark
57
narrow histone mark
33
chromatin remodeller
2
other context
2
other post-translational modification
Date released
315
November, 2017
August, 2021
78
February, 2021
68
August, 2017
64
May, 2021
61
November, 2018
39
December, 2017
39
February, 2018
28
December, 2018
23
January, 2019
19
October, 2019
17
February, 2023
5
January, 2018
5
March, 2020
2
March, 2023
1
August, 2018
1
May, 2020
1
October, 2022
Available data
665
bam
586
bigWig
564
fastq
463
bed narrowPeak
372
bigBed narrowPeak
97
tsv
60
bed broadPeak
60
bigBed broadPeak
37
tagAlign
24
bed bed3+
6
bed bed3
6
bed bedgraph
3
tar
3
txt
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
Organism
762
Homo sapiens
Biosample type
2457
tissue
1030
primary cell
529
cell line
237
in vitro differentiated cells
9
stem cell
Organ
385
liver
89
connective tissue
67
heart
66
artery
66
blood vessel
66
vasculature
61
blood
61
bodily fluid
23
embryo
22
epithelium
19
pancreas
2
kidney
1
adipose tissue
1
mammary gland
Project
759
AMP
5
T1D
2
community
Genome assembly (visualization)
603
hg19
535
GRCh38
4
hg18
Lab
710
AMP-T2D consortium
52
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
2
Struan F.A. Grant, CHOP
Audit category:
inconsistent ontology term
2
audit script error
1
inconsistent control
1
inconsistent replicate
Audit category:
19
missing controlled_by
Audit category:
42
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
audit.ERROR.category!
inconsistent ontology term
month_released!
August, 2021
BIOSAMPLE
ASSAY
766 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
GRO-seq
CRISPR genome editing followed by DNA sequencing
DNase-seq
Hi-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
360
5
1
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
EndoC_BH1
3
2
1
+ See 7 more…
in vitro differentiated cells
adipocyte
67
5
7
1
embryonic stem cell
40
7
6
1
pancreatic endoderm
18
4
1
hepatocyte
15
definitive endodermal cell
8
2
1
+ See 16 more…
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