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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
453
ChIP-seq
109
total RNA-seq
13
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
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
453
DNA binding
111
Transcription
15
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
89
recombinant protein
83
control
65
RNA binding protein
37
histone
37
histone modification
chromatin remodeller
19
broad histone mark
18
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
300
November, 2017
96
February, 2021
54
November, 2018
44
August, 2021
30
October, 2019
26
December, 2018
May, 2021
17
January, 2019
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
547
bam
487
bigWig
397
fastq
373
bed narrowPeak
325
bigBed narrowPeak
115
tsv
55
bed broadPeak
55
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
607
Homo sapiens
Biosample type
2735
tissue
881
primary cell
611
cell line
255
in vitro differentiated cells
9
stem cell
Organ
381
liver
71
pancreas
66
artery
66
blood vessel
66
heart
66
vasculature
58
epithelium
51
blood
51
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
601
AMP
8
T1D
2
community
Genome assembly (visualization)
495
hg19
431
GRCh38
Lab
564
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:
71
inconsistent ontology term
1
inconsistent replicate
Audit category:
7
missing controlled_by
Audit category:
15
inconsistent control read length
1
inconsistent assembly
month_released!
May, 2021
assembly!
hg18
target.investigated_as!
chromatin remodeller
BIOSAMPLE
ASSAY
611 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
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
358
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
EndoC_BH1
14
29
3
6
1
3
2
2
1
GM12878
50
1
Panc1
13
1
1
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