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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
417
ChIP-seq
113
total RNA-seq
28
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
417
DNA binding
115
Transcription
29
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
312
transcription factor
89
recombinant protein
79
control
61
RNA binding protein
26
chromatin remodeller
24
histone
24
histone modification
13
narrow histone mark
11
broad histone mark
3
nucleotide modification
1
other context
1
other post-translational modification
Date released
256
November, 2017
88
February, 2021
61
November, 2018
44
August, 2021
29
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
January, 2018
1
May, 2020
1
October, 2022
Available data
582
bam
521
bigWig
427
fastq
404
bed narrowPeak
355
bigBed narrowPeak
119
tsv
59
bed broadPeak
bigBed broadPeak
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
589
Homo sapiens
Biosample type
2361
tissue
950
primary cell
593
cell line
349
in vitro differentiated cells
9
stem cell
Organ
342
liver
91
pancreas
79
epithelium
60
artery
60
blood
60
blood vessel
60
bodily fluid
60
heart
60
vasculature
19
kidney
8
embryo
1
mammary gland
Project
582
AMP
9
T1D
2
community
Genome assembly (visualization)
464
hg19
414
GRCh38
Lab
546
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
92
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
13
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
month_released!
January, 2018
files.file_type!
bigBed broadPeak
tagAlign
BIOSAMPLE
ASSAY
593 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
319
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
GM12878
60
smooth muscle cell of the coronary artery
52
8
Panc1
13
1
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