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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
483
ChIP-seq
101
total RNA-seq
26
ATAC-seq
6
MeRIP-seq
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
2
HiChIP
2
pCHi-C
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
483
DNA binding
103
Transcription
28
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
37
histone
37
histone modification
30
chromatin remodeller
19
broad histone mark
18
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
95
February, 2021
61
November, 2018
36
August, 2021
30
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
568
bam
507
bigWig
427
fastq
402
bed narrowPeak
355
bigBed narrowPeak
102
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
638
Homo sapiens
Biosample type
2737
tissue
1087
primary cell
642
cell line
357
in vitro differentiated cells
6
stem cell
Organ
400
liver
87
pancreas
74
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
17
kidney
embryo
Project
634
AMP
6
T1D
2
community
Genome assembly (visualization)
514
hg19
450
GRCh38
Lab
595
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:
85
inconsistent ontology term
1
inconsistent control
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
audit.ERROR.category!
inconsistent replicate
month_released!
March, 2020
organ_slims!
embryo
BIOSAMPLE
ASSAY
642 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
pCHi-C
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
14
2
2
2
1
1
EndoC_BH1
14
31
17
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
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