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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
466
ChIP-seq
28
ATAC-seq
6
MeRIP-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
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
Assay category
466
DNA binding
30
DNA accessibility
3
3D chromatin structure
2
Transcription
1
DNA methylation
Target of assay
350
transcription factor
89
recombinant protein
79
control
64
RNA binding protein
35
histone
35
histone modification
30
chromatin remodeller
18
broad histone mark
17
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
November, 2018
28
December, 2018
26
October, 2019
18
February, 2021
18
January, 2019
17
May, 2021
15
November, 2019
6
February, 2023
6
November, 2020
2
August, 2021
2
March, 2020
2
March, 2023
1
January, 2018
1
October, 2022
Available data
582
bam
508
bigWig
427
fastq
390
bed narrowPeak
355
bigBed narrowPeak
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
Organism
514
Homo sapiens
Biosample type
1658
tissue
818
primary cell
518
cell line
263
in vitro differentiated cells
6
stem cell
Organ
364
liver
61
blood
61
bodily fluid
58
pancreas
44
epithelium
14
artery
14
blood vessel
14
heart
14
vasculature
11
kidney
Project
509
AMP
7
T1D
2
community
Genome assembly (visualization)
410
hg19
360
GRCh38
Lab
505
AMP-T2D consortium
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
52
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
files.file_type!
tsv
lab.title!
Bing Ren, UCSD
BIOSAMPLE
ASSAY
518 results
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Clear Filters
ChIP-seq
ATAC-seq
MeRIP-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
pCHi-C
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
360
1
1
1
1
GM12878
60
1
EndoC_BH1
15
18
6
3
1
2
2
1
Panc1
13
1
1
smooth muscle cell of the coronary artery
6
8
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