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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
406
ChIP-seq
47
total RNA-seq
20
ATAC-seq
6
MeRIP-seq
4
Hi-C
2
Capture-C
2
STARR-seq
2
pCHi-C
1
CRISPR genome editing followed by sgRNA sequencing
1
DNase-seq
1
WGBS
1
whole genome sequencing assay
Assay category
406
DNA binding
47
Transcription
21
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
298
transcription factor
82
recombinant protein
71
control
55
RNA binding protein
37
histone
37
histone modification
20
chromatin remodeller
19
broad histone mark
18
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
46
November, 2018
33
August, 2021
28
February, 2021
21
May, 2021
16
November, 2019
15
October, 2019
6
November, 2020
5
January, 2019
5
March, 2020
1
December, 2018
1
February, 2023
1
May, 2020
Available data
429
bam
388
bigWig
367
fastq
329
bed narrowPeak
300
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
49
tsv
12
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
vcf
Organism
492
Homo sapiens
Biosample type
866
tissue
493
cell line
360
primary cell
18
in vitro differentiated cells
Organ
401
liver
92
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
489
AMP
4
T1D
Genome assembly (visualization)
388
hg19
323
GRCh38
Lab
456
AMP-T2D consortium
31
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
Audit category:
76
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!
HiChIP
organ_slims!
adrenal gland
BIOSAMPLE
ASSAY
493 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
Hi-C
Capture-C
STARR-seq
pCHi-C
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
WGBS
whole genome sequencing assay
cell line
HepG2
378
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
2
1
Panc1
13
1
1
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