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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
463
ChIP-seq
109
total RNA-seq
13
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
463
DNA binding
111
Transcription
15
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
356
transcription factor
89
recombinant protein
79
control
65
RNA binding protein
30
chromatin remodeller
26
histone
26
histone modification
13
broad histone mark
13
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
303
November, 2017
88
February, 2021
61
November, 2018
44
August, 2021
30
October, 2019
28
December, 2018
23
January, 2019
May, 2021
16
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
577
bam
517
bigWig
427
fastq
403
bed narrowPeak
355
bigBed narrowPeak
115
tsv
59
bed broadPeak
59
bigBed broadPeak
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
617
Homo sapiens
Biosample type
2459
tissue
866
primary cell
621
cell line
228
in vitro differentiated cells
10
stem cell
Organ
389
liver
71
pancreas
61
blood
61
bodily fluid
60
artery
60
blood vessel
60
heart
60
vasculature
58
epithelium
19
kidney
8
embryo
1
mammary gland
Project
611
AMP
8
T1D
2
community
Genome assembly (visualization)
508
hg19
445
GRCh38
Lab
574
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
71
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
15
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
month_released!
May, 2021
files.file_type!
tagAlign
BIOSAMPLE
ASSAY
621 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
366
14
1
2
2
2
1
1
EndoC_BH1
14
29
3
6
1
3
2
2
1
GM12878
60
1
smooth muscle cell of the coronary artery
52
8
Panc1
13
1
1
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