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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
377
ChIP-seq
104
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
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
Assay category
377
DNA binding
106
Transcription
31
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
350
transcription factor
recombinant protein
79
control
64
RNA binding protein
35
histone
35
histone modification
30
chromatin remodeller
18
broad histone mark
17
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
249
November, 2017
96
February, 2021
45
November, 2018
28
December, 2018
23
January, 2019
23
October, 2019
21
May, 2021
16
November, 2019
11
March, 2020
10
August, 2021
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
493
bam
420
bigWig
345
fastq
302
bed narrowPeak
274
bigBed narrowPeak
110
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
Organism
535
Homo sapiens
Biosample type
2773
tissue
1088
primary cell
539
cell line
355
in vitro differentiated cells
10
stem cell
Organ
288
liver
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
10
kidney
8
embryo
1
mammary gland
Project
528
AMP
9
T1D
2
community
Genome assembly (visualization)
430
hg19
376
GRCh38
Lab
526
AMP-T2D consortium
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
84
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
month_released!
February, 2018
lab.title!
Bing Ren, UCSD
target.investigated_as!
recombinant protein
BIOSAMPLE
ASSAY
539 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
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
cell line
HepG2
278
5
1
2
1
1
EndoC_BH1
15
33
19
6
3
1
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
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