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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
385
ChIP-seq
113
total RNA-seq
28
ATAC-seq
6
pCHi-C
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
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
385
DNA binding
115
Transcription
30
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
295
transcription factor
88
recombinant protein
74
control
49
RNA binding protein
26
histone
26
histone modification
13
broad histone mark
narrow histone mark
9
chromatin remodeller
2
other context
2
other post-translational modification
Date released
292
November, 2017
96
February, 2021
42
August, 2021
41
November, 2018
27
October, 2019
20
May, 2021
12
November, 2019
10
March, 2020
6
February, 2023
5
January, 2019
2
March, 2023
1
December, 2018
1
May, 2020
1
October, 2022
Available data
485
bam
428
bigWig
339
fastq
313
bed narrowPeak
272
bigBed narrowPeak
119
tsv
45
bed broadPeak
45
bigBed broadPeak
9
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
552
Homo sapiens
Biosample type
2446
tissue
965
primary cell
556
cell line
324
in vitro differentiated cells
8
stem cell
Organ
371
liver
77
pancreas
67
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
60
blood
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
547
AMP
7
T1D
2
community
Genome assembly (visualization)
436
hg19
377
GRCh38
Lab
517
AMP-T2D consortium
32
Bing Ren, UCSD
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
80
inconsistent ontology term
1
inconsistent replicate
Audit category:
7
missing controlled_by
Audit category:
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
audit.WARNING.category!
inconsistent control read length
lab.title!
Rohit N. Kulkarni, M.D., Ph.D.
organ_slims!
bodily fluid
target.investigated_as!
narrow histone mark
BIOSAMPLE
ASSAY
556 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
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
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
348
14
1
2
2
2
1
1
EndoC_BH1
9
33
19
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
Panc1
10
1
1
H1-hESC
8
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