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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
113
total RNA-seq
92
ChIP-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
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
115
Transcription
92
DNA binding
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
83
control
9
transcription factor
3
histone
3
histone modification
3
nucleotide modification
2
RNA binding protein
2
broad histone mark
1
narrow histone mark
1
recombinant protein
Date released
82
February, 2021
66
November, 2017
30
August, 2021
15
October, 2019
8
January, 2019
8
March, 2020
6
February, 2023
6
November, 2020
5
November, 2018
4
May, 2021
4
November, 2019
2
March, 2023
1
December, 2018
1
May, 2020
October, 2022
Available data
570
bam
517
bigWig
427
fastq
bed narrowPeak
353
bigBed narrowPeak
118
tsv
58
bed broadPeak
58
bigBed broadPeak
20
tagAlign
3
tar
2
bed bed3+
2
bedpe bed3+
2
hic
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
vcf
Organism
235
Homo sapiens
Biosample type
1712
tissue
347
primary cell
241
in vitro differentiated cells
238
cell line
8
stem cell
Organ
93
liver
54
artery
54
blood vessel
54
heart
54
vasculature
53
pancreas
46
epithelium
11
kidney
8
embryo
6
blood
6
bodily fluid
1
mammary gland
Project
229
AMP
7
T1D
2
community
Genome assembly (visualization)
127
hg19
106
GRCh38
Lab
205
AMP-T2D consortium
20
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
Audit category:
1
missing controlled_by
Audit category:
2
inconsistent control read length
1
inconsistent assembly
assay_slims!
DNA accessibility
files.file_type!
bed narrowPeak
lab.title!
Klaus Kaestner, Upenn
month_released!
October, 2022
BIOSAMPLE
ASSAY
238 results
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total RNA-seq
ChIP-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
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
14
71
2
2
2
1
1
smooth muscle cell of the coronary artery
52
2
EndoC_BH1
33
2
6
1
3
2
2
1
H1-hESC
8
Panc1
7
1
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