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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
399
ChIP-seq
113
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
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
399
DNA binding
115
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
356
transcription factor
89
recombinant protein
79
control
RNA binding protein
30
chromatin remodeller
27
histone
27
histone modification
14
narrow histone mark
13
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
269
November, 2017
88
February, 2021
40
November, 2018
38
August, 2021
30
October, 2019
26
December, 2018
21
May, 2021
17
January, 2019
15
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
518
bam
459
bigWig
364
fastq
341
bed narrowPeak
294
bigBed narrowPeak
119
tsv
55
bed broadPeak
55
bigBed broadPeak
tagAlign
3
bed bed3+
2
bedpe bed3+
2
hic
2
tar
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
568
Homo sapiens
Biosample type
2505
tissue
935
primary cell
572
cell line
343
in vitro differentiated cells
10
stem cell
Organ
333
liver
91
pancreas
78
epithelium
60
artery
60
blood vessel
60
heart
60
vasculature
51
blood
51
bodily fluid
17
kidney
8
embryo
1
mammary gland
Project
561
AMP
9
T1D
2
community
Genome assembly (visualization)
451
hg19
392
GRCh38
Lab
531
AMP-T2D consortium
28
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
90
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
11
missing controlled_by
Audit category:
9
inconsistent control read length
5
inconsistent control run_type
1
inconsistent assembly
assay_title!
STARR-seq
files.file_type!
tagAlign
month_released!
April, 2018
target.investigated_as!
RNA binding protein
BIOSAMPLE
ASSAY
572 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
312
14
1
2
2
1
1
EndoC_BH1
14
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
52
8
GM12878
50
1
Panc1
13
1
1
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