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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
96
total RNA-seq
6
MeRIP-seq
6
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
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
98
Transcription
DNA accessibility
3
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
August, 2021
28
December, 2018
28
October, 2019
23
January, 2019
15
November, 2019
9
March, 2020
6
February, 2023
6
November, 2020
5
May, 2021
2
March, 2023
1
May, 2020
1
October, 2022
Available data
562
bam
495
bigWig
427
fastq
378
bed narrowPeak
353
bigBed narrowPeak
101
tsv
58
bed broadPeak
58
bigBed broadPeak
20
tagAlign
3
tar
2
bed bed3+
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
Organism
583
Homo sapiens
Biosample type
2148
tissue
795
primary cell
587
cell line
321
in vitro differentiated cells
10
stem cell
Organ
369
liver
70
pancreas
60
blood
60
bodily fluid
58
artery
58
blood vessel
58
heart
58
vasculature
57
epithelium
16
kidney
1
mammary gland
Project
576
AMP
9
T1D
2
community
Genome assembly (visualization)
492
hg19
444
GRCh38
Lab
574
AMP-T2D consortium
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
70
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
assay_title!
DNAme array
month_released!
August, 2021
BIOSAMPLE
ASSAY
587 results
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ChIP-seq
total RNA-seq
MeRIP-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
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
1
2
1
GM12878
60
smooth muscle cell of the coronary artery
6
52
Panc1
13
1
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