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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
453
ChIP-seq
103
total RNA-seq
28
ATAC-seq
6
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
2
Hi-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
Assay category
453
DNA binding
103
Transcription
30
DNA accessibility
2
3D chromatin structure
1
DNA methylation
Target of assay
349
transcription factor
89
recombinant protein
74
control
63
RNA binding protein
30
chromatin remodeller
25
histone
25
histone modification
13
narrow histone mark
12
broad histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
96
February, 2021
61
November, 2018
30
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
November, 2019
11
March, 2020
10
August, 2021
6
February, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
567
bam
496
bigWig
427
fastq
378
bed narrowPeak
355
bigBed narrowPeak
109
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
Organism
602
Homo sapiens
Biosample type
2437
tissue
763
primary cell
604
cell line
382
in vitro differentiated cells
8
stem cell
Organ
370
liver
70
pancreas
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
57
epithelium
17
kidney
8
embryo
1
mammary gland
Project
595
AMP
9
T1D
Genome assembly (visualization)
501
hg19
451
GRCh38
Lab
599
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:
69
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!
November, 2019
BIOSAMPLE
ASSAY
604 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
Hi-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
cell line
HepG2
360
5
1
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
EndoC_BH1
2
32
18
3
2
2
1
Panc1
13
1
1
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