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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
713
total RNA-seq
221
ChIP-seq
87
ATAC-seq
11
snATAC-seq
10
DNase-seq
10
MeRIP-seq
10
WGBS
6
Hi-C
6
single cell RNA-seq
4
small RNA-seq
3
pCHi-C
2
Capture-C
2
FAIRE-seq
2
RRBS
1
CRISPR genome editing followed by sgRNA sequencing
1
RNA microarray
Assay category
723
Transcription
221
DNA binding
110
DNA accessibility
12
DNA methylation
6
3D chromatin structure
Target of assay
125
histone
125
histone modification
71
broad histone mark
65
control
54
narrow histone mark
36
transcription factor
14
RNA binding protein
5
nucleotide modification
Date released
412
February, 2021
204
August, 2017
120
July, 2018
74
October, 2018
61
May, 2021
56
November, 2019
24
May, 2022
20
February, 2023
19
October, 2019
16
July, 2019
15
March, 2020
10
November, 2020
8
January, 2021
8
November, 2018
6
April, 2018
6
October, 2017
6
September, 2017
5
August, 2021
5
June, 2019
5
March, 2019
3
February, 2020
2
May, 2019
1
August, 2018
1
August, 2022
1
January, 2018
1
May, 2023
Available data
935
bam
854
bigWig
708
tsv
257
fastq
159
bed narrowPeak
79
bigBed narrowPeak
35
bed bed3+
27
tagAlign
24
bed broadPeak
9
bigBed broadPeak
8
bed bedMethyl
8
bigBed bedMethyl
6
txt
5
bedpe bed3+
4
hic
1
bedpe
1
hdf5
Organism
1080
Homo sapiens
Biosample type
993
tissue
primary cell
92
cell line
4
in vitro differentiated cells
Organ
777
liver
645
connective tissue
600
pancreas
489
adipose tissue
380
heart
318
kidney
265
brain
199
blood vessel
199
vasculature
158
bone element
139
artery
122
limb
118
epithelium
82
musculature of body
61
blood
61
bodily fluid
56
eye
43
nerve
37
embryo
25
spleen
20
lung
18
ureter
16
skeleton
5
gonad
5
ovary
2
intestine
2
pituitary gland
2
thymus
1
adrenal gland
1
esophagus
1
large intestine
1
lymph node
1
mammary gland
pericardium
1
skin of body
1
small intestine
1
spinal cord
1
stomach
1
urinary bladder
Project
1055
AMP
34
T1D
Genome assembly (visualization)
897
hg19
865
GRCh38
Lab
1020
AMP-T2D consortium
51
Kyle Gaulton, UCSD
10
Rohit N. Kulkarni, M.D., Ph.D.
4
Bing Ren, UCSD
2
Mark McCarthy, Oxford
1
Maike Sander, UCSD
1
Stephen Parker, UMich
Audit category:
77
inconsistent ontology term
1
audit script error
Audit category:
22
missing controlled_by
Audit category:
5
inconsistent control read length
2
inconsistent assembly
organ_slims!
pericardium
biosample_type!
primary cell
BIOSAMPLE
ASSAY
1089 results
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total RNA-seq
ChIP-seq
ATAC-seq
snATAC-seq
DNase-seq
MeRIP-seq
WGBS
Hi-C
single cell RNA-seq
small RNA-seq
pCHi-C
Capture-C
FAIRE-seq
RRBS
CRISPR genome editing followed by sgRNA sequencing
RNA microarray
tissue
islet of Langerhans
278
50
58
7
1
4
3
6
1
1
adipose tissue
382
2
3
3
1
body of pancreas
3
35
4
4
2
2
subcutaneous abdominal adipose tissue
36
3
pancreas
2
16
4
2
2
1
1
1
1
+ See 6 more…
cell line
EndoC_BH1
33
15
19
6
1
2
1
Panc1
13
1
1
in vitro differentiated cells
pancreatic PP cell
3
white fat cell
1
See all biosamples
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