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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
456
ChIP-seq
104
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
4
Hi-C
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
STARR-seq
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
456
DNA binding
106
Transcription
30
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
340
transcription factor
82
recombinant protein
77
control
59
RNA binding protein
37
histone
37
histone modification
24
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
96
February, 2021
61
November, 2018
42
August, 2021
28
December, 2018
January, 2019
21
May, 2021
16
November, 2019
15
October, 2019
9
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
544
bam
490
bigWig
404
fastq
381
bed narrowPeak
339
bigBed narrowPeak
108
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
616
Homo sapiens
Biosample type
2470
tissue
1050
primary cell
620
cell line
394
in vitro differentiated cells
10
stem cell
Organ
396
liver
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
43
blood
43
bodily fluid
kidney
8
embryo
1
mammary gland
Project
609
AMP
9
T1D
2
community
Genome assembly (visualization)
498
hg19
432
GRCh38
Lab
575
AMP-T2D consortium
32
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
77
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
month_released!
January, 2019
files.file_type!
csv
organ_slims!
kidney
BIOSAMPLE
ASSAY
620 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
Hi-C
pCHi-C
CRISPR genome editing followed by DNA sequencing
STARR-seq
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
378
9
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
42
1
Panc1
13
1
1
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