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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
144
ChIP-seq
77
total RNA-seq
10
ATAC-seq
4
STARR-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-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
144
DNA binding
79
Transcription
12
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
112
transcription factor
30
RNA binding protein
19
control
16
recombinant protein
15
chromatin remodeller
11
histone
11
histone modification
6
narrow histone mark
5
broad histone mark
Date released
November, 2017
70
February, 2021
61
November, 2018
41
August, 2021
28
December, 2018
23
January, 2019
17
October, 2019
6
February, 2023
4
March, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
206
bam
196
bigWig
134
bed narrowPeak
112
fastq
106
bigBed narrowPeak
80
tsv
8
tagAlign
3
bed bed3+
1
bed bed3
1
bed bedMethyl
1
bed broadPeak
1
bedpe bed3+
1
bigBed bedMethyl
1
bigBed broadPeak
1
hdf5
1
hic
1
txt
1
vcf
Organism
251
Homo sapiens
Biosample type
2461
tissue
1025
primary cell
279
in vitro differentiated cells
255
cell line
9
stem cell
Organ
86
liver
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
16
pancreas
8
embryo
4
kidney
3
epithelium
1
mammary gland
Project
248
AMP
5
T1D
2
community
Genome assembly (visualization)
204
hg19
190
GRCh38
Lab
215
AMP-T2D consortium
33
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
3
missing controlled_by
Audit category:
5
inconsistent control read length
4
inconsistent control run_type
1
inconsistent assembly
audit.ERROR.category!
inconsistent ontology term
lab.title!
Katalin Susztak, Upenn
Maike Sander, UCSD
month_released!
November, 2017
BIOSAMPLE
ASSAY
255 results
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ChIP-seq
total RNA-seq
ATAC-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-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
63
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
H1-hESC
8
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