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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
148
ATAC-seq
105
ChIP-seq
104
total RNA-seq
87
single cell RNA-seq
56
snATAC-seq
47
WGBS
23
pCHi-C
10
RRBS
9
Hi-C
6
MeRIP-seq
5
STARR-seq
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
DNAme array
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
206
DNA accessibility
193
Transcription
105
DNA binding
58
DNA methylation
9
3D chromatin structure
1
DNA sequencing
Target of assay
95
control
8
histone
8
histone modification
5
broad histone mark
5
transcription factor
3
narrow histone mark
3
nucleotide modification
2
RNA binding protein
1
recombinant protein
Date released
134
May, 2022
94
February, 2023
59
February, 2021
58
May, 2020
56
September, 2020
51
May, 2021
47
November, 2017
23
August, 2021
21
October, 2019
13
August, 2017
9
July, 2019
8
January, 2021
8
June, 2019
7
November, 2020
5
March, 2020
5
November, 2018
4
November, 2019
4
October, 2022
3
January, 2019
3
March, 2023
1
December, 2018
1
May, 2019
1
September, 2018
Available data
1191
bam
bigWig
836
fastq
699
bed narrowPeak
464
bigBed narrowPeak
389
tsv
153
zippedFastqFolder
120
tagAlign
108
bed broadPeak
108
bigBed broadPeak
40
bed bed3+
11
bed bedMethyl
11
bigBed bedMethyl
8
hic
6
bedpe bed3+
5
hdf5
4
tar
3
cool
2
bed bed3
2
csv
1
txt
1
vcf
Organism
611
Homo sapiens
Biosample type
1005
tissue
475
primary cell
140
cell line
135
in vitro differentiated cells
7
stem cell
Organ
204
epithelium
190
pancreas
72
liver
18
vasculature
17
blood vessel
15
kidney
14
blood
14
bodily fluid
13
heart
10
artery
7
connective tissue
7
vein
3
musculature of body
2
eye
1
bone element
1
bone marrow
1
brain
1
mammary gland
Project
314
HPAP
269
AMP
29
T1D
2
community
1
ITG
Genome assembly (visualization)
45
hg19
27
GRCh38
Lab
314
Klaus Kaestner, Upenn
243
AMP-T2D consortium
29
Kyle Gaulton, UCSD
20
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
1
ITG
Audit category:
50
inconsistent ontology term
31
audit script error
1
inconsistent replicate
Audit category:
1
missing controlled_by
files.file_type!
bigWig
BIOSAMPLE
ASSAY
615 results
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Clear Filters
ATAC-seq
ChIP-seq
total RNA-seq
single cell RNA-seq
snATAC-seq
WGBS
pCHi-C
RRBS
Hi-C
MeRIP-seq
STARR-seq
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
DNAme array
MPRA
shRNA RNA-seq
siRNA RNA-seq
...and 1 more
primary cell
Langerhans cell
85
48
pancreatic alpha cell
22
6
42
31
1
pancreatic beta cell
13
6
11
16
1
exocrine cell
39
naive thymus-derived CD4-positive, alpha-beta T cell
22
2
1
1
+ See 41 more…
cell line
HepG2
1
52
9
2
2
2
EndoC_BH1
17
2
1
6
3
2
2
1
smooth muscle cell of the coronary artery
8
2
Panc1
7
GM12878
6
+ See 11 more…
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