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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
458
ChIP-seq
113
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
5
STARR-seq
5
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
458
DNA binding
115
Transcription
30
DNA accessibility
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
346
transcription factor
88
recombinant protein
83
control
59
RNA binding protein
27
histone
27
histone modification
19
chromatin remodeller
14
narrow histone mark
13
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
294
November, 2017
95
February, 2021
56
November, 2018
43
August, 2021
28
October, 2019
27
December, 2018
23
January, 2019
21
May, 2021
15
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
556
bam
495
bigWig
400
fastq
380
bed narrowPeak
331
bigBed narrowPeak
119
tsv
46
bed broadPeak
46
bigBed broadPeak
9
tagAlign
3
tar
bed bed3+
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
txt
1
vcf
Organism
626
Homo sapiens
Biosample type
2510
tissue
1040
primary cell
630
cell line
356
in vitro differentiated cells
7
stem cell
Organ
372
liver
89
pancreas
78
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
619
AMP
9
T1D
2
community
Genome assembly (visualization)
499
hg19
440
GRCh38
Lab
584
AMP-T2D consortium
33
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
91
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
8
missing controlled_by
Audit category:
inconsistent control read length
8
inconsistent control run_type
files.file_type!
bed bed3+
audit.WARNING.category!
inconsistent control read length
assay_slims!
3D chromatin structure
BIOSAMPLE
ASSAY
630 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
352
14
1
2
1
1
1
EndoC_BH1
15
33
19
6
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
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