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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
382
ChIP-seq
76
total RNA-seq
10
ATAC-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
2
Hi-C
2
HiChIP
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
382
DNA binding
78
Transcription
10
DNA accessibility
2
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
353
transcription factor
82
recombinant protein
69
control
RNA binding protein
30
chromatin remodeller
19
histone
19
histone modification
10
narrow histone mark
9
broad histone mark
2
other context
2
other post-translational modification
Date released
281
November, 2017
70
February, 2021
41
August, 2021
40
November, 2018
26
December, 2018
17
January, 2019
October, 2019
6
March, 2020
5
February, 2023
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
441
bam
392
bigWig
364
fastq
313
bed narrowPeak
286
bigBed narrowPeak
81
tsv
54
bed broadPeak
54
bigBed broadPeak
20
tagAlign
2
tar
1
bed bed3
1
bed bed3+
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hic
1
txt
1
vcf
Organism
488
Homo sapiens
Biosample type
2013
tissue
698
primary cell
491
cell line
372
in vitro differentiated cells
10
stem cell
Organ
347
liver
76
epithelium
pancreas
66
artery
66
blood vessel
66
heart
66
vasculature
51
blood
51
bodily fluid
8
embryo
4
kidney
1
mammary gland
Project
484
AMP
5
T1D
2
community
Genome assembly (visualization)
399
hg19
340
GRCh38
Lab
451
AMP-T2D consortium
33
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
3
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
11
missing controlled_by
Audit category:
20
inconsistent control read length
5
inconsistent control run_type
organ_slims!
pancreas
month_released!
October, 2019
target.investigated_as!
RNA binding protein
BIOSAMPLE
ASSAY
491 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
HiChIP
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
324
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
50
1
H1-hESC
8
EndoC_BH1
3
2
EndoC-BH1
1
1
HEK293T
2
early embryonic cell
2
iPSC derived cell line
2
MCF-7
1
MIN6
1
RCC 7860 VHL
1
RCC 7860 vector
1
Synthesized DNA
1
fibroblast cell line
1
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