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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
469
ChIP-seq
110
total RNA-seq
28
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
3
Hi-C
2
Capture-C
2
DNase-seq
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
469
DNA binding
112
Transcription
30
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
360
transcription factor
89
recombinant protein
81
control
64
RNA binding protein
30
chromatin remodeller
26
histone
26
histone modification
13
broad histone mark
13
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
96
February, 2021
61
November, 2018
44
August, 2021
30
October, 2019
28
December, 2018
23
January, 2019
20
May, 2021
November, 2019
8
March, 2020
6
November, 2020
2
March, 2023
1
February, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
563
bam
506
bigWig
427
fastq
390
bed narrowPeak
355
bigBed narrowPeak
116
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
1
vcf
Organism
633
Homo sapiens
Biosample type
2666
tissue
884
primary cell
637
cell line
389
in vitro differentiated cells
10
stem cell
Organ
401
liver
72
pancreas
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
59
epithelium
19
kidney
8
embryo
1
mammary gland
Project
635
AMP
T1D
2
community
Genome assembly (visualization)
512
hg19
447
GRCh38
Lab
595
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
Audit category:
72
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
month_released!
November, 2019
award.project!
T1D
BIOSAMPLE
ASSAY
637 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
Capture-C
DNase-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
EndoC_BH1
30
18
6
2
1
Panc1
13
1
1
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