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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
399
ChIP-seq
77
total RNA-seq
10
ATAC-seq
4
STARR-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
DNase-seq
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
399
DNA binding
79
Transcription
12
DNA accessibility
3
3D chromatin structure
1
DNA sequencing
Target of assay
296
transcription factor
72
control
66
recombinant protein
43
RNA binding protein
26
histone
26
histone modification
23
chromatin remodeller
13
broad histone mark
13
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
70
February, 2021
November, 2018
41
August, 2021
28
December, 2018
23
January, 2019
17
October, 2019
6
February, 2023
4
March, 2020
2
March, 2023
1
January, 2018
1
May, 2020
Available data
459
bam
407
bigWig
366
fastq
327
bed narrowPeak
299
bigBed narrowPeak
80
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bedpe bed3+
1
hdf5
1
hic
txt
1
vcf
Organism
505
Homo sapiens
Biosample type
2585
tissue
1033
primary cell
508
cell line
277
in vitro differentiated cells
9
stem cell
Organ
355
liver
66
artery
66
blood vessel
66
heart
66
vasculature
46
blood
46
bodily fluid
16
pancreas
8
embryo
4
kidney
3
epithelium
1
mammary gland
Project
501
AMP
5
T1D
2
community
Genome assembly (visualization)
416
hg19
350
GRCh38
Lab
468
AMP-T2D consortium
33
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
10
missing controlled_by
Audit category:
21
inconsistent control read length
4
inconsistent control run_type
1
inconsistent assembly
audit.ERROR.category!
inconsistent ontology term
files.file_type!
txt
month_released!
November, 2018
target.investigated_as!
nucleotide modification
BIOSAMPLE
ASSAY
508 results
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ChIP-seq
total RNA-seq
ATAC-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
333
14
1
2
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
45
1
Panc1
13
1
1
H1-hESC
8
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