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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
441
ChIP-seq
68
total RNA-seq
10
ATAC-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
2
DNase-seq
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
Hi-C
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
Assay category
441
DNA binding
70
Transcription
12
DNA accessibility
1
3D chromatin structure
1
DNA methylation
Target of assay
342
transcription factor
82
recombinant protein
71
control
63
RNA binding protein
30
chromatin remodeller
23
histone
23
histone modification
12
broad histone mark
11
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
70
February, 2021
61
November, 2018
28
December, 2018
23
January, 2019
16
October, 2019
8
August, 2021
6
February, 2023
4
March, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
520
bam
449
bigWig
427
fastq
369
bed narrowPeak
355
bigBed narrowPeak
71
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
tar
2
bed bed3+
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
txt
Organism
532
Homo sapiens
Biosample type
2681
tissue
1032
primary cell
536
cell line
279
in vitro differentiated cells
9
stem cell
Organ
370
liver
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
15
pancreas
8
embryo
3
epithelium
2
kidney
1
mammary gland
Project
529
AMP
5
T1D
2
community
Genome assembly (visualization)
454
hg19
406
GRCh38
Lab
529
AMP-T2D consortium
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
inconsistent assembly
audit.WARNING.category!
inconsistent assembly
audit.ERROR.category!
inconsistent ontology term
lab.title!
Bing Ren, UCSD
BIOSAMPLE
ASSAY
536 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
Hi-C
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
360
5
1
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
H1-hESC
8
EndoC_BH1
3
2
1
EndoC-BH1
1
1
early embryonic cell
2
glomerular visceral epithelial cell
1
1
iPSC derived cell line
2
MCF-7
1
MIN6
1
fibroblast cell line
1
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