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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
394
ChIP-seq
113
total RNA-seq
29
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
394
DNA binding
115
Transcription
31
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
336
transcription factor
89
recombinant protein
83
control
RNA binding protein
38
histone
38
histone modification
28
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
281
November, 2017
96
February, 2021
43
August, 2021
40
November, 2018
30
October, 2019
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
493
bam
434
bigWig
338
fastq
316
bed narrowPeak
269
bigBed narrowPeak
119
tsv
55
bed broadPeak
55
bigBed broadPeak
20
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
567
Homo sapiens
Biosample type
2742
tissue
918
primary cell
571
cell line
383
in vitro differentiated cells
10
stem cell
Organ
346
liver
91
pancreas
78
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
26
blood
26
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
560
AMP
9
T1D
2
community
Genome assembly (visualization)
443
hg19
381
GRCh38
Lab
525
AMP-T2D consortium
33
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
91
inconsistent ontology term
1
inconsistent replicate
Audit category:
11
missing controlled_by
Audit category:
20
inconsistent control read length
5
inconsistent control run_type
1
inconsistent assembly
files.file_type!
zippedFastqFolder
month_released!
August, 2020
December, 2018
target.investigated_as!
RNA binding protein
BIOSAMPLE
ASSAY
571 results
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ChIP-seq
total RNA-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
324
14
1
2
2
1
1
1
EndoC_BH1
14
33
19
6
3
1
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
25
1
Panc1
13
1
1
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