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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
474
ChIP-seq
109
total RNA-seq
6
MeRIP-seq
4
Hi-C
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
STARR-seq
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
Assay category
474
DNA binding
111
Transcription
DNA accessibility
4
3D chromatin structure
1
DNA methylation
Target of assay
354
transcription factor
82
recombinant protein
80
control
65
RNA binding protein
38
histone
38
histone modification
30
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
87
February, 2021
61
November, 2018
41
August, 2021
28
December, 2018
23
January, 2019
15
November, 2019
14
October, 2019
7
March, 2020
6
February, 2023
6
November, 2020
5
May, 2021
2
March, 2023
1
May, 2020
1
October, 2022
Available data
556
bam
506
bigWig
427
fastq
385
bed narrowPeak
353
bigBed narrowPeak
112
tsv
58
bed broadPeak
58
bigBed broadPeak
20
tagAlign
3
tar
2
bed bed3+
2
bedpe bed3+
2
hic
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
vcf
Organism
608
Homo sapiens
Biosample type
2158
tissue
776
primary cell
612
cell line
351
in vitro differentiated cells
10
stem cell
Organ
399
liver
72
pancreas
60
blood
60
bodily fluid
59
epithelium
58
artery
58
blood vessel
58
heart
58
vasculature
kidney
8
embryo
1
mammary gland
Project
601
AMP
9
T1D
2
community
Genome assembly (visualization)
504
hg19
441
GRCh38
Lab
568
AMP-T2D consortium
31
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
58
inconsistent ontology term
1
inconsistent control
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_slims!
DNA accessibility
organ_slims!
kidney
files.file_type!
vcf
BIOSAMPLE
ASSAY
612 results
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Clear Filters
ChIP-seq
total RNA-seq
MeRIP-seq
Hi-C
pCHi-C
CRISPR genome editing followed by DNA sequencing
STARR-seq
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
378
14
2
2
2
1
EndoC_BH1
15
33
6
1
3
2
2
1
GM12878
60
smooth muscle cell of the coronary artery
6
52
Panc1
13
1
H1-hESC
8
EndoC-BH1
1
1
early embryonic cell
2
iPSC derived cell line
2
MCF-7
1
MIN6
1
Synthesized DNA
1
fibroblast cell line
1
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