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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
112
total RNA-seq
111
ChIP-seq
28
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
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
114
Transcription
111
DNA binding
30
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
transcription factor
89
recombinant protein
81
control
64
RNA binding protein
30
chromatin remodeller
28
histone
28
histone modification
15
narrow histone mark
13
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
91
February, 2021
74
November, 2017
33
August, 2021
23
October, 2019
21
May, 2021
November, 2019
11
March, 2020
9
January, 2019
6
February, 2023
6
November, 2020
4
November, 2018
3
December, 2018
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
219
bam
155
bigWig
118
tsv
90
fastq
41
bed narrowPeak
27
bigBed narrowPeak
15
bed broadPeak
15
bigBed broadPeak
15
tagAlign
3
bed bed3+
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
1
vcf
Organism
282
Homo sapiens
Biosample type
2641
tissue
1078
primary cell
340
in vitro differentiated cells
286
cell line
10
stem cell
Organ
104
liver
76
pancreas
63
epithelium
62
artery
62
blood vessel
62
heart
62
vasculature
12
kidney
10
blood
10
bodily fluid
8
embryo
1
mammary gland
Project
275
AMP
9
T1D
2
community
Genome assembly (visualization)
165
hg19
143
GRCh38
Lab
250
AMP-T2D consortium
23
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
69
inconsistent ontology term
1
inconsistent replicate
Audit category:
1
missing controlled_by
Audit category:
11
inconsistent control read length
1
inconsistent assembly
organ_slims!
pituitary gland
target.investigated_as!
transcription factor
month_released!
November, 2019
BIOSAMPLE
ASSAY
286 results
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total RNA-seq
ChIP-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
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
14
81
1
2
2
2
1
1
EndoC_BH1
32
2
18
6
3
2
2
1
smooth muscle cell of the coronary artery
52
2
8
Panc1
13
1
1
GM12878
9
1
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