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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
429
ChIP-seq
108
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
429
DNA binding
110
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
347
transcription factor
89
recombinant protein
80
control
59
RNA binding protein
37
histone
histone modification
24
chromatin remodeller
19
broad histone mark
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
300
November, 2017
96
February, 2021
61
November, 2018
41
August, 2021
28
December, 2018
23
October, 2019
January, 2019
20
May, 2021
10
March, 2020
6
November, 2019
6
November, 2020
4
February, 2023
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
525
bam
466
bigWig
389
fastq
355
bed narrowPeak
321
bigBed narrowPeak
114
tsv
45
bed broadPeak
45
bigBed broadPeak
9
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
596
Homo sapiens
Biosample type
2148
tissue
851
primary cell
600
cell line
282
in vitro differentiated cells
8
stem cell
Organ
378
liver
73
pancreas
67
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
43
blood
43
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
593
AMP
5
T1D
2
community
Genome assembly (visualization)
474
hg19
413
GRCh38
Lab
558
AMP-T2D consortium
31
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
3
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
80
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
12
missing controlled_by
Audit category:
15
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_title!
HiChIP
month_released!
January, 2019
target.investigated_as!
histone modification
narrow histone mark
BIOSAMPLE
ASSAY
600 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
360
9
1
2
2
2
1
1
EndoC_BH1
3
33
19
6
1
3
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
42
1
H1-hESC
8
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