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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
372
ChIP-seq
104
total RNA-seq
29
ATAC-seq
6
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
3
MeRIP-seq
2
Capture-C
2
DNase-seq
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
Assay category
372
DNA binding
106
Transcription
31
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
350
transcription factor
89
recombinant protein
control
64
RNA binding protein
35
histone
35
histone modification
30
chromatin remodeller
broad histone mark
17
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
251
November, 2017
93
February, 2021
58
November, 2018
28
December, 2018
21
May, 2021
20
January, 2019
17
October, 2019
11
March, 2020
10
August, 2021
8
November, 2019
6
February, 2023
3
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
488
bam
478
bigWig
374
bed narrowPeak
357
fastq
345
bigBed narrowPeak
110
tsv
51
bed broadPeak
51
bigBed broadPeak
10
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
Organism
527
Homo sapiens
Biosample type
2283
tissue
931
primary cell
531
cell line
301
in vitro differentiated cells
8
stem cell
Organ
306
liver
71
pancreas
68
epithelium
64
artery
64
blood vessel
64
heart
64
vasculature
55
blood
55
bodily fluid
14
kidney
8
embryo
1
mammary gland
Project
520
AMP
9
T1D
2
community
Genome assembly (visualization)
485
hg19
448
GRCh38
Lab
521
AMP-T2D consortium
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
3
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
Audit category:
77
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
20
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
target.investigated_as!
control
broad histone mark
lab.title!
Bing Ren, UCSD
BIOSAMPLE
ASSAY
531 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
MeRIP-seq
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
296
5
1
2
1
1
EndoC_BH1
7
33
19
3
1
3
2
2
1
smooth muscle cell of the coronary artery
4
52
8
GM12878
54
1
H1-hESC
8
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