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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
426
ChIP-seq
80
total RNA-seq
10
ATAC-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
2
Hi-C
2
HiChIP
1
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
426
DNA binding
82
Transcription
11
DNA accessibility
2
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
360
transcription factor
89
recombinant protein
72
control
64
RNA binding protein
chromatin remodeller
19
histone
19
histone modification
10
narrow histone mark
9
broad histone mark
2
other context
2
other post-translational modification
Date released
300
November, 2017
70
February, 2021
54
November, 2018
42
August, 2021
26
December, 2018
17
January, 2019
15
October, 2019
6
March, 2020
5
February, 2023
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
489
bam
436
bigWig
397
fastq
353
bed narrowPeak
318
bigBed narrowPeak
85
tsv
54
bed broadPeak
54
bigBed broadPeak
20
tagAlign
3
tar
1
bed bed3
1
bed bed3+
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hic
1
txt
1
vcf
Organism
537
Homo sapiens
Biosample type
2230
tissue
741
primary cell
540
cell line
388
in vitro differentiated cells
10
stem cell
Organ
381
liver
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
51
blood
51
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
533
AMP
5
T1D
2
community
Genome assembly (visualization)
442
hg19
381
GRCh38
Lab
499
AMP-T2D consortium
34
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
16
inconsistent ontology term
1
inconsistent replicate
Audit category:
7
missing controlled_by
Audit category:
15
inconsistent control read length
organ_slims!
pancreas
target.investigated_as!
chromatin remodeller
BIOSAMPLE
ASSAY
540 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
HiChIP
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
358
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
50
1
H1-hESC
8
EndoC_BH1
3
2
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