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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
453
ChIP-seq
80
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
1
whole genome sequencing assay
Assay category
453
DNA binding
82
Transcription
11
DNA accessibility
2
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
357
transcription factor
89
recombinant protein
72
control
63
RNA binding protein
30
chromatin remodeller
19
histone
19
histone modification
10
narrow histone mark
9
broad histone mark
2
other context
2
other post-translational modification
Date released
312
November, 2017
70
February, 2021
61
November, 2018
42
August, 2021
28
December, 2018
23
January, 2019
15
October, 2019
6
March, 2020
5
February, 2023
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
519
bam
466
bigWig
427
fastq
383
bed narrowPeak
348
bigBed narrowPeak
85
tsv
58
bed broadPeak
58
bigBed broadPeak
20
tagAlign
tar
1
bed bed3
1
bed bed3+
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hic
1
txt
1
vcf
Organism
564
Homo sapiens
Biosample type
2185
tissue
741
primary cell
567
cell line
391
in vitro differentiated cells
10
stem cell
Organ
398
liver
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
560
AMP
5
T1D
2
community
Genome assembly (visualization)
469
hg19
409
GRCh38
Lab
526
AMP-T2D consortium
34
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
16
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
assay_title!
RNA microarray
files.file_type!
tar
organ_slims!
pancreas
BIOSAMPLE
ASSAY
567 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
whole genome sequencing assay
cell line
HepG2
375
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
H1-hESC
8
EndoC_BH1
3
2
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