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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
461
ChIP-seq
79
total RNA-seq
10
ATAC-seq
5
STARR-seq
5
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
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
461
DNA binding
81
Transcription
11
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
352
transcription factor
89
recombinant protein
78
control
61
RNA binding protein
26
histone
26
histone modification
22
chromatin remodeller
13
broad histone mark
13
narrow histone mark
2
other context
2
other post-translational modification
Date released
311
November, 2017
70
February, 2021
57
November, 2018
42
August, 2021
28
December, 2018
28
October, 2019
23
January, 2019
6
March, 2020
5
February, 2023
2
March, 2023
1
January, 2018
May, 2020
1
October, 2022
Available data
523
bam
464
bigWig
419
fastq
381
bed narrowPeak
346
bigBed narrowPeak
83
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
1
vcf
Organism
571
Homo sapiens
Biosample type
2565
tissue
574
cell line
534
primary cell
370
in vitro differentiated cells
10
stem cell
Organ
392
liver
92
pancreas
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
567
AMP
5
T1D
2
community
Genome assembly (visualization)
470
hg19
409
GRCh38
Lab
533
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:
7
missing controlled_by
Audit category:
26
inconsistent control read length
inconsistent control run_type
1
inconsistent assembly
assay_title!
FAIRE-seq
audit.WARNING.category!
inconsistent control run_type
month_released!
May, 2020
organ_slims!
epithelium
BIOSAMPLE
ASSAY
574 results
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ChIP-seq
total RNA-seq
ATAC-seq
STARR-seq
pCHi-C
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
370
14
1
2
1
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
H1-hESC
8
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