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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
482
ChIP-seq
107
total RNA-seq
13
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
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
482
DNA binding
109
Transcription
15
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
89
recombinant protein
83
control
65
RNA binding protein
36
histone
36
histone modification
30
chromatin remodeller
19
broad histone mark
17
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
96
February, 2021
61
November, 2018
44
August, 2021
30
October, 2019
28
December, 2018
23
January, 2019
May, 2021
16
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
574
bam
514
bigWig
427
fastq
402
bed narrowPeak
355
bigBed narrowPeak
113
tsv
59
bed broadPeak
59
bigBed broadPeak
20
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
629
Homo sapiens
Biosample type
2706
tissue
829
primary cell
633
cell line
262
in vitro differentiated cells
10
stem cell
Organ
401
liver
68
pancreas
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
55
epithelium
19
kidney
8
embryo
1
mammary gland
Project
631
AMP
T1D
2
community
Genome assembly (visualization)
522
hg19
456
GRCh38
Lab
591
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
Audit category:
68
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
1
inconsistent assembly
organ_slims!
spinal cord
award.project!
T1D
month_released!
May, 2021
BIOSAMPLE
ASSAY
633 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
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
378
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
EndoC_BH1
13
27
3
6
1
2
1
Panc1
13
1
1
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