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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
426
ChIP-seq
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
5
STARR-seq
5
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
426
DNA binding
30
DNA accessibility
3
3D chromatin structure
2
Transcription
1
DNA methylation
1
DNA sequencing
Target of assay
317
transcription factor
89
recombinant protein
83
control
61
RNA binding protein
26
chromatin remodeller
24
histone
24
histone modification
13
narrow histone mark
11
broad histone mark
3
nucleotide modification
1
other context
1
other post-translational modification
Date released
257
November, 2017
61
November, 2018
28
December, 2018
27
August, 2021
24
October, 2019
18
January, 2019
17
February, 2021
17
May, 2021
15
November, 2019
7
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
478
bam
422
fastq
418
bigWig
404
bed narrowPeak
355
bigBed narrowPeak
59
bed broadPeak
bigBed broadPeak
20
tagAlign
6
tsv
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
484
Homo sapiens
Biosample type
1535
tissue
784
primary cell
488
cell line
232
in vitro differentiated cells
7
stem cell
Organ
328
liver
61
blood
61
bodily fluid
57
pancreas
45
epithelium
15
kidney
14
artery
14
blood vessel
14
heart
14
vasculature
1
mammary gland
Project
479
AMP
7
T1D
2
community
Genome assembly (visualization)
365
hg19
314
GRCh38
Lab
450
AMP-T2D consortium
25
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
56
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
13
inconsistent control read length
8
inconsistent control run_type
files.file_type!
bed bed3+
bigBed broadPeak
assay_title!
total RNA-seq
BIOSAMPLE
ASSAY
488 results
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ChIP-seq
ATAC-seq
MeRIP-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
320
1
2
1
2
1
1
GM12878
60
1
EndoC_BH1
15
19
6
3
1
2
2
1
smooth muscle cell of the coronary artery
6
8
Panc1
13
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