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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
375
ChIP-seq
108
total RNA-seq
29
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
DNase-seq
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
375
DNA binding
110
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA sequencing
Target of assay
347
transcription factor
recombinant protein
80
control
59
RNA binding protein
37
histone
37
histone modification
24
chromatin remodeller
19
broad histone mark
18
narrow histone mark
3
nucleotide modification
other context
2
other post-translational modification
Date released
247
November, 2017
96
February, 2021
44
August, 2021
44
November, 2018
28
December, 2018
January, 2019
23
October, 2019
21
May, 2021
16
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
468
bam
412
bigWig
320
fastq
299
bed narrowPeak
257
bigBed narrowPeak
114
tsv
58
bed broadPeak
58
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
543
Homo sapiens
Biosample type
2742
tissue
1078
primary cell
547
cell line
394
in vitro differentiated cells
10
stem cell
Organ
311
liver
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
43
blood
43
bodily fluid
12
kidney
8
embryo
1
mammary gland
Project
536
AMP
9
T1D
2
community
Genome assembly (visualization)
423
hg19
353
GRCh38
Lab
500
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:
85
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
12
missing controlled_by
Audit category:
25
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
files.file_type!
bigBed bedMethyl
month_released!
January, 2019
target.investigated_as!
other context
recombinant protein
BIOSAMPLE
ASSAY
547 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
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
294
9
1
2
2
2
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
42
1
Panc1
13
1
1
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