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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
466
ChIP-seq
104
total RNA-seq
6
MeRIP-seq
6
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
Hi-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
466
DNA binding
106
Transcription
DNA accessibility
2
3D chromatin structure
1
DNA methylation
Target of assay
350
transcription factor
89
recombinant protein
79
control
64
RNA binding protein
35
histone
35
histone modification
30
chromatin remodeller
18
broad histone mark
17
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
28
December, 2018
27
October, 2019
23
January, 2019
15
November, 2019
10
August, 2021
9
March, 2020
6
February, 2023
6
November, 2020
5
May, 2021
2
March, 2023
1
May, 2020
1
October, 2022
Available data
570
bam
502
bigWig
427
fastq
378
bed narrowPeak
353
bigBed narrowPeak
109
tsv
58
bed broadPeak
58
bigBed broadPeak
20
tagAlign
3
tar
1
bed bed3+
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hic
1
txt
Organism
592
Homo sapiens
Biosample type
2263
tissue
798
primary cell
596
cell line
351
in vitro differentiated cells
10
stem cell
Organ
369
liver
71
pancreas
60
blood
60
bodily fluid
59
epithelium
58
artery
58
blood vessel
58
heart
58
vasculature
16
kidney
8
embryo
1
mammary gland
Project
585
AMP
9
T1D
2
community
Genome assembly (visualization)
499
hg19
451
GRCh38
Lab
583
AMP-T2D consortium
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
72
inconsistent ontology term
1
inconsistent control
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
inconsistent assembly
assay_slims!
DNA accessibility
audit.WARNING.category!
inconsistent assembly
lab.title!
Bing Ren, UCSD
BIOSAMPLE
ASSAY
596 results
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ChIP-seq
total RNA-seq
MeRIP-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
Hi-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
360
5
2
1
1
EndoC_BH1
15
33
6
3
2
1
2
1
GM12878
60
smooth muscle cell of the coronary artery
6
52
Panc1
13
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