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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
451
ChIP-seq
113
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
451
DNA binding
115
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
344
transcription factor
88
recombinant protein
79
control
63
RNA binding protein
26
histone
26
histone modification
24
chromatin remodeller
13
broad histone mark
13
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
293
November, 2017
88
February, 2021
58
November, 2018
44
August, 2021
30
October, 2019
28
December, 2018
23
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
569
bam
510
bigWig
414
fastq
392
bed narrowPeak
343
bigBed narrowPeak
119
tsv
59
bed broadPeak
59
bigBed broadPeak
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
625
Homo sapiens
Biosample type
2477
tissue
944
primary cell
629
cell line
348
in vitro differentiated cells
10
stem cell
Organ
376
liver
92
pancreas
79
epithelium
61
blood
61
bodily fluid
60
artery
60
blood vessel
60
heart
60
vasculature
19
kidney
8
embryo
1
mammary gland
Project
618
AMP
9
T1D
2
community
Genome assembly (visualization)
501
hg19
445
GRCh38
Lab
582
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:
missing controlled_by
Audit category:
10
inconsistent control read length
2
inconsistent control run_type
1
inconsistent assembly
files.file_type!
tagAlign
audit.NOT_COMPLIANT.category!
missing controlled_by
BIOSAMPLE
ASSAY
629 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
353
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
GM12878
60
1
smooth muscle cell of the coronary artery
52
8
Panc1
13
1
1
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