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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
351
ChIP-seq
113
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
351
DNA binding
115
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA sequencing
Target of assay
304
transcription factor
80
control
recombinant protein
44
RNA binding protein
38
histone
38
histone modification
23
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
249
November, 2017
96
February, 2021
November, 2018
44
August, 2021
28
December, 2018
23
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
448
bam
392
bigWig
300
fastq
275
bed narrowPeak
233
bigBed narrowPeak
119
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
hdf5
1
txt
1
vcf
Organism
524
Homo sapiens
Biosample type
2746
tissue
1087
primary cell
528
cell line
394
in vitro differentiated cells
10
stem cell
Organ
289
liver
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
46
blood
46
bodily fluid
12
kidney
8
embryo
1
mammary gland
Project
517
AMP
9
T1D
2
community
Genome assembly (visualization)
404
hg19
334
GRCh38
Lab
481
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:
10
missing controlled_by
Audit category:
20
inconsistent control read length
4
inconsistent control run_type
1
inconsistent assembly
month_released!
November, 2018
organ_slims!
ovary
target.investigated_as!
recombinant protein
BIOSAMPLE
ASSAY
528 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
267
14
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
45
1
Panc1
13
1
1
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