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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
464
ChIP-seq
113
total RNA-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
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
Assay category
464
DNA binding
115
Transcription
DNA accessibility
4
3D chromatin structure
1
DNA methylation
Target of assay
356
transcription factor
89
recombinant protein
79
control
65
RNA binding protein
30
chromatin remodeller
27
histone
27
histone modification
14
narrow histone mark
13
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
303
November, 2017
79
February, 2021
61
November, 2018
43
August, 2021
28
December, 2018
28
October, 2019
23
January, 2019
15
November, 2019
9
March, 2020
6
February, 2023
6
November, 2020
5
May, 2021
2
March, 2023
1
May, 2020
1
October, 2022
Available data
570
bam
517
bigWig
427
fastq
392
bed narrowPeak
353
bigBed narrowPeak
118
tsv
58
bed broadPeak
58
bigBed broadPeak
tagAlign
3
tar
2
bed bed3+
2
bedpe bed3+
2
hic
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
vcf
Organism
606
Homo sapiens
Biosample type
2069
tissue
700
primary cell
610
cell line
311
in vitro differentiated cells
10
stem cell
Organ
387
liver
72
pancreas
60
blood
60
bodily fluid
59
epithelium
52
artery
52
blood vessel
52
heart
52
vasculature
18
kidney
8
embryo
1
mammary gland
Project
599
AMP
9
T1D
2
community
Genome assembly (visualization)
498
hg19
438
GRCh38
Lab
564
AMP-T2D consortium
33
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
73
inconsistent ontology term
1
inconsistent control
Audit category:
13
missing controlled_by
Audit category:
15
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_slims!
DNA accessibility
files.file_type!
vcf
tagAlign
BIOSAMPLE
ASSAY
610 results
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Clear Filters
ChIP-seq
total RNA-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
366
14
2
2
2
1
EndoC_BH1
15
33
6
1
3
2
2
1
GM12878
60
smooth muscle cell of the coronary artery
52
Panc1
13
1
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