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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
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
193
Transcription
105
DNA binding
58
DNA accessibility
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
95
May, 2022
82
February, 2023
56
September, 2020
50
February, 2021
47
November, 2017
23
August, 2021
22
May, 2021
19
October, 2019
13
August, 2017
9
July, 2019
8
January, 2021
8
June, 2019
6
November, 2020
5
March, 2020
5
November, 2018
4
October, 2022
3
January, 2019
3
March, 2023
3
May, 2020
3
November, 2019
1
December, 2018
1
May, 2019
1
September, 2018
Available data
1097
bam
bigWig
804
fastq
650
bed narrowPeak
442
bigBed narrowPeak
376
tsv
120
tagAlign
114
zippedFastqFolder
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
csv
1
txt
1
vcf
Organism
463
Homo sapiens
Biosample type
788
tissue
353
primary cell
114
cell line
105
in vitro differentiated cells
7
stem cell
Organ
147
epithelium
134
pancreas
70
liver
15
kidney
14
blood
14
bodily fluid
10
vasculature
9
blood vessel
7
vein
6
connective tissue
5
heart
3
musculature of body
2
artery
2
eye
1
bone element
1
bone marrow
1
brain
1
mammary gland
Project
275
HPAP
160
AMP
29
T1D
2
community
1
ITG
Genome assembly (visualization)
19
hg19
1
GRCh38
Lab
275
Klaus Kaestner, Upenn
134
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:
31
audit script error
25
inconsistent ontology term
Audit category:
1
missing controlled_by
files.file_type!
bigWig
assay_title!
ATAC-seq
BIOSAMPLE
ASSAY
467 results
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Clear Filters
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
whole genome sequencing assay
primary cell
Langerhans cell
85
48
pancreatic alpha cell
6
42
31
1
exocrine cell
39
pancreatic beta cell
6
11
16
1
peripheral blood mononuclear cell
8
+ See 34 more…
cell line
HepG2
52
9
2
2
2
1
EndoC_BH1
2
1
6
3
2
2
1
Panc1
7
GM12878
6
EndoC-BH1
1
1
+ See 11 more…
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