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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
469
ChIP-seq
111
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
2
Capture-C
2
DNase-seq
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
469
DNA binding
113
Transcription
31
DNA accessibility
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
349
transcription factor
88
recombinant protein
83
control
63
RNA binding protein
35
histone
35
histone modification
24
chromatin remodeller
19
broad histone mark
16
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
305
November, 2017
96
February, 2021
58
November, 2018
43
August, 2021
29
October, 2019
27
December, 2018
23
January, 2019
20
May, 2021
15
November, 2019
8
March, 2020
6
November, 2020
2
March, 2023
1
February, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
565
bam
505
bigWig
413
fastq
390
bed narrowPeak
343
bigBed narrowPeak
117
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
1
vcf
Organism
632
Homo sapiens
Biosample type
2686
tissue
782
primary cell
636
cell line
384
in vitro differentiated cells
10
stem cell
Organ
386
liver
86
pancreas
74
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
634
AMP
T1D
2
community
Genome assembly (visualization)
511
hg19
454
GRCh38
Lab
595
AMP-T2D consortium
33
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
Audit category:
87
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
missing controlled_by
Audit category:
21
inconsistent control read length
2
inconsistent control run_type
assay_slims!
3D chromatin structure
assay_title!
snATAC-seq
audit.NOT_COMPLIANT.category!
missing controlled_by
award.project!
T1D
BIOSAMPLE
ASSAY
636 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
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
365
14
1
2
2
1
1
EndoC_BH1
13
31
19
6
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
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