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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
469
ChIP-seq
104
total RNA-seq
29
ATAC-seq
10
pCHi-C
3
Hi-C
2
Capture-C
2
DNase-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
GRO-seq
1
MPRA
1
WGBS
Assay category
469
DNA binding
104
Transcription
31
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
350
transcription factor
89
recombinant protein
77
control
64
RNA binding protein
37
histone
37
histone modification
30
chromatin remodeller
19
broad histone mark
18
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
96
February, 2021
61
November, 2018
30
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
15
March, 2020
10
August, 2021
3
December, 2017
2
January, 2018
1
February, 2023
1
May, 2020
1
October, 2022
Available data
585
bam
511
bigWig
431
fastq
392
bed narrowPeak
355
bigBed narrowPeak
114
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
6
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
Organism
621
Homo sapiens
Biosample type
2424
tissue
615
cell line
524
primary cell
340
in vitro differentiated cells
8
stem cell
Organ
370
liver
86
pancreas
73
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
17
kidney
8
embryo
1
connective tissue
1
mammary gland
Project
619
AMP
4
T1D
Genome assembly (visualization)
518
hg19
467
GRCh38
1
hg18
Lab
623
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
4
Anna Gloyn, Oxford
Audit category:
86
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
28
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
lab.title!
Xin Sun, UCSD
organ_slims!
urinary bladder
BIOSAMPLE
ASSAY
623 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
Hi-C
Capture-C
DNase-seq
CRISPR genome editing followed by sgRNA sequencing
GRO-seq
MPRA
WGBS
cell line
HepG2
360
5
1
2
1
1
EndoC_BH1
15
33
19
1
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
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stem cell
hESC
3
1
mesenchymal stem cell
1
mesendoderm
1
neural progenitor cell (neural stem cell)
1
trophoblast
1
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