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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
392
ChIP-seq
113
total RNA-seq
28
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
2
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
392
DNA binding
115
Transcription
30
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
298
transcription factor
88
recombinant protein
77
control
53
RNA binding protein
36
histone
36
histone modification
broad histone mark
17
narrow histone mark
14
chromatin remodeller
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
297
November, 2017
96
February, 2021
43
August, 2021
43
November, 2018
26
October, 2019
21
May, 2021
11
March, 2020
10
November, 2019
6
February, 2023
6
November, 2020
5
January, 2019
2
March, 2023
1
December, 2018
1
May, 2020
1
October, 2022
Available data
491
bam
437
bigWig
346
fastq
321
bed narrowPeak
279
bigBed narrowPeak
119
tsv
51
bed broadPeak
51
bigBed broadPeak
14
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
565
Homo sapiens
Biosample type
2450
tissue
935
primary cell
569
cell line
332
in vitro differentiated cells
9
stem cell
Organ
379
liver
82
pancreas
73
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
558
AMP
9
T1D
2
community
Genome assembly (visualization)
445
hg19
389
GRCh38
Lab
523
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:
86
inconsistent ontology term
1
inconsistent replicate
Audit category:
missing controlled_by
Audit category:
15
inconsistent control read length
2
inconsistent control run_type
1
inconsistent assembly
audit.NOT_COMPLIANT.category!
missing controlled_by
organ_slims!
bodily fluid
thymus
target.investigated_as!
broad histone mark
BIOSAMPLE
ASSAY
569 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
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
356
14
1
2
2
2
1
1
EndoC_BH1
9
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
Panc1
9
1
1
H1-hESC
8
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