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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
442
ChIP-seq
79
total RNA-seq
10
ATAC-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
2
Hi-C
2
HiChIP
1
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
whole genome sequencing assay
Assay category
442
DNA binding
81
Transcription
11
DNA accessibility
2
3D chromatin structure
1
DNA methylation
Target of assay
335
transcription factor
89
recombinant protein
78
control
62
RNA binding protein
28
chromatin remodeller
26
histone
26
histone modification
13
broad histone mark
13
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
70
February, 2021
61
November, 2018
41
August, 2021
December, 2018
28
October, 2019
23
January, 2019
6
March, 2020
5
February, 2023
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
504
bam
445
bigWig
399
fastq
362
bed narrowPeak
327
bigBed narrowPeak
84
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
551
Homo sapiens
Biosample type
2755
tissue
682
primary cell
554
cell line
368
in vitro differentiated cells
10
stem cell
Organ
399
liver
92
pancreas
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
34
blood
34
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
547
AMP
5
T1D
2
community
Genome assembly (visualization)
451
hg19
388
GRCh38
Lab
514
AMP-T2D consortium
33
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
16
inconsistent ontology term
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_title!
whole genome sequencing assay
files.file_type!
ibed
month_released!
December, 2018
organ_slims!
epithelium
BIOSAMPLE
ASSAY
554 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
HiChIP
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
378
14
1
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
33
1
Panc1
13
1
1
H1-hESC
8
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