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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
440
ChIP-seq
108
total RNA-seq
29
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
440
DNA binding
110
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
332
transcription factor
88
recombinant protein
80
control
53
RNA binding protein
26
histone
26
histone modification
13
broad histone mark
13
chromatin remodeller
13
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
294
November, 2017
96
February, 2021
56
November, 2018
44
August, 2021
30
October, 2019
28
December, 2018
January, 2019
21
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
533
bam
476
bigWig
378
fastq
365
bed narrowPeak
316
bigBed narrowPeak
114
tsv
46
bed broadPeak
46
bigBed broadPeak
9
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
609
Homo sapiens
Biosample type
2724
tissue
1083
primary cell
613
cell line
377
in vitro differentiated cells
8
stem cell
Organ
370
liver
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
43
blood
43
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
602
AMP
9
T1D
2
community
Genome assembly (visualization)
484
hg19
422
GRCh38
Lab
566
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:
92
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
8
missing controlled_by
Audit category:
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
audit.WARNING.category!
inconsistent control read length
month_released!
January, 2019
BIOSAMPLE
ASSAY
613 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
352
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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