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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
471
ChIP-seq
28
ATAC-seq
6
MeRIP-seq
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
pCHi-C
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
471
DNA binding
30
DNA accessibility
4
3D chromatin structure
2
Transcription
1
DNA methylation
1
DNA sequencing
Target of assay
349
transcription factor
88
recombinant protein
83
control
63
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
305
November, 2017
58
November, 2018
28
December, 2018
27
August, 2021
26
October, 2019
18
February, 2021
18
January, 2019
17
May, 2021
15
November, 2019
6
February, 2023
6
November, 2020
2
March, 2020
2
March, 2023
1
January, 2018
1
October, 2022
Available data
569
bam
510
bigWig
414
fastq
392
bed narrowPeak
343
bigBed narrowPeak
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
526
Homo sapiens
Biosample type
1674
tissue
774
primary cell
530
cell line
257
in vitro differentiated cells
6
stem cell
Organ
373
liver
61
blood
61
bodily fluid
58
pancreas
44
epithelium
14
artery
14
blood vessel
14
heart
14
vasculature
13
kidney
Project
521
AMP
7
T1D
2
community
Genome assembly (visualization)
413
hg19
355
GRCh38
Lab
492
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:
53
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
missing controlled_by
Audit category:
21
inconsistent control read length
2
inconsistent control run_type
1
inconsistent assembly
audit.NOT_COMPLIANT.category!
missing controlled_by
files.file_type!
tsv
lab.title!
Maike Sander, UCSD
BIOSAMPLE
ASSAY
530 results
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ChIP-seq
ATAC-seq
MeRIP-seq
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
pCHi-C
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
365
1
2
2
1
1
1
GM12878
60
1
EndoC_BH1
15
18
6
1
3
2
2
1
Panc1
13
1
1
smooth muscle cell of the coronary artery
6
8
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