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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
464
ChIP-seq
113
total RNA-seq
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
464
DNA binding
115
Transcription
4
3D chromatin structure
2
DNA accessibility
1
DNA methylation
1
DNA sequencing
Target of assay
356
transcription factor
89
recombinant protein
79
control
65
RNA binding protein
30
chromatin remodeller
27
histone
27
histone modification
14
narrow histone mark
13
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
303
November, 2017
79
February, 2021
61
November, 2018
44
August, 2021
30
October, 2019
28
December, 2018
23
January, 2019
15
November, 2019
9
March, 2020
6
February, 2023
6
November, 2020
5
May, 2021
2
March, 2023
1
May, 2020
1
October, 2022
Available data
572
bam
519
bigWig
427
fastq
394
bed narrowPeak
355
bigBed narrowPeak
118
tsv
59
bed broadPeak
59
bigBed broadPeak
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
609
Homo sapiens
Biosample type
2275
tissue
787
primary cell
613
cell line
312
in vitro differentiated cells
10
stem cell
Organ
388
liver
73
pancreas
60
blood
60
bodily fluid
60
epithelium
52
artery
52
blood vessel
52
heart
52
vasculature
19
kidney
8
embryo
1
mammary gland
Project
602
AMP
9
T1D
2
community
Genome assembly (visualization)
500
hg19
440
GRCh38
Lab
566
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:
73
inconsistent ontology term
1
inconsistent control
Audit category:
13
missing controlled_by
Audit category:
15
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_title!
ATAC-seq
FAIRE-seq
files.file_type!
tagAlign
lab.title!
Stephen Parker, UMich
BIOSAMPLE
ASSAY
613 results
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ChIP-seq
total RNA-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
366
14
2
2
2
1
1
EndoC_BH1
15
33
6
1
3
2
2
1
GM12878
60
smooth muscle cell of the coronary artery
52
Panc1
13
1
1
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