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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
466
ChIP-seq
104
total RNA-seq
29
ATAC-seq
6
pCHi-C
3
Hi-C
2
Capture-C
2
DNase-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
Assay category
466
DNA binding
104
Transcription
31
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
350
transcription factor
89
recombinant protein
76
control
64
RNA binding protein
35
histone
35
histone modification
30
chromatin remodeller
18
broad histone mark
17
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
11
March, 2020
10
August, 2021
1
February, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
582
bam
508
bigWig
427
fastq
390
bed narrowPeak
355
bigBed narrowPeak
110
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
Organism
613
Homo sapiens
Biosample type
2414
tissue
615
cell line
514
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
mammary gland
Project
611
AMP
4
T1D
Genome assembly (visualization)
515
hg19
464
GRCh38
Lab
615
AMP-T2D consortium
33
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
1
Anna Gloyn, Oxford
Audit category:
85
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
assay_slims!
DNA sequencing
assay_title!
RRBS
shRNA RNA-seq
BIOSAMPLE
ASSAY
615 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
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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