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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
114
total RNA-seq
90
ATAC-seq
74
single cell RNA-seq
47
WGBS
23
ChIP-seq
6
MeRIP-seq
5
Hi-C
2
Capture-C
1
CRISPR genome editing followed by sgRNA sequencing
1
DNase-seq
Assay category
188
Transcription
91
DNA accessibility
47
DNA methylation
23
DNA binding
5
3D chromatin structure
Target of assay
78
histone
histone modification
41
narrow histone mark
37
broad histone mark
24
control
3
nucleotide modification
2
transcription factor
1
RNA binding protein
Date released
80
May, 2022
40
September, 2018
38
February, 2023
37
July, 2018
33
April, 2018
32
February, 2021
22
May, 2021
19
September, 2020
15
August, 2017
8
October, 2019
7
August, 2020
6
November, 2019
6
November, 2020
5
September, 2017
4
March, 2020
3
August, 2018
3
October, 2022
2
August, 2021
2
October, 2018
1
June, 2018
Available data
200
fastq
182
bam
173
bigWig
142
tsv
80
zippedFastqFolder
26
bed narrowPeak
23
bigBed narrowPeak
4
bedpe bed3+
4
hic
3
cool
2
bed bed3+
2
tagAlign
1
bed broadPeak
1
bigBed broadPeak
1
hdf5
Organism
362
Homo sapiens
Biosample type
tissue
288
primary cell
73
cell line
2
in vitro differentiated cells
Organ
416
epithelium
397
liver
363
pancreas
92
connective tissue
86
vasculature
81
blood vessel
78
heart
68
artery
68
blood
68
bodily fluid
45
kidney
25
embryo
18
brain
7
vein
6
musculature of body
4
eye
3
adipose tissue
1
bone element
1
bone marrow
1
mammary gland
1
pericardium
Project
209
AMP
152
HPAP
2
T1D
Genome assembly (visualization)
172
GRCh38
168
hg19
Lab
205
AMP-T2D consortium
152
Klaus Kaestner, Upenn
6
Rohit N. Kulkarni, M.D., Ph.D.
Audit category:
69
inconsistent ontology term
3
audit script error
Audit category:
1
inconsistent assembly
biosample_type!
tissue
target.investigated_as!
histone modification
BIOSAMPLE
ASSAY
363 results
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total RNA-seq
ATAC-seq
single cell RNA-seq
WGBS
ChIP-seq
MeRIP-seq
Hi-C
Capture-C
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
primary cell
pancreatic alpha cell
52
35
12
31
6
1
pancreatic beta cell
21
23
12
16
6
1
pancreatic acinar cell
4
9
12
1
pancreatic ductal cell
4
4
10
pancreatic delta cell
11
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cell line
EndoC_BH1
33
19
3
6
1
2
1
Panc1
6
1
1
in vitro differentiated cells
pancreatic PP cell
2
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