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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
401
total RNA-seq
152
ATAC-seq
148
ChIP-seq
74
single cell RNA-seq
51
WGBS
11
snATAC-seq
10
MeRIP-seq
9
Hi-C
8
DNase-seq
2
Capture-C
2
FAIRE-seq
2
RRBS
2
small RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
pCHi-C
Assay category
477
Transcription
173
DNA accessibility
148
DNA binding
53
DNA methylation
9
3D chromatin structure
Target of assay
106
histone
106
histone modification
55
narrow histone mark
51
broad histone mark
39
control
8
transcription factor
5
nucleotide modification
3
RNA binding protein
Date released
172
August, 2017
157
July, 2018
104
May, 2022
72
September, 2018
58
May, 2021
56
February, 2023
55
November, 2019
October, 2018
39
April, 2018
32
February, 2021
19
September, 2020
18
October, 2019
14
March, 2020
11
September, 2017
10
November, 2020
8
January, 2021
7
August, 2020
7
November, 2018
6
July, 2019
5
March, 2019
5
October, 2017
4
August, 2021
4
June, 2019
3
August, 2018
3
October, 2022
2
May, 2019
1
August, 2022
1
February, 2020
1
June, 2018
Available data
636
bam
581
bigWig
434
fastq
415
tsv
174
bed narrowPeak
80
zippedFastqFolder
51
bigBed narrowPeak
29
bed bed3+
21
bed broadPeak
tagAlign
7
bedpe bed3+
7
bigBed broadPeak
7
hic
6
bed bedMethyl
6
bigBed bedMethyl
6
txt
3
cool
1
bedpe
1
hdf5
Organism
873
Homo sapiens
Biosample type
438
tissue
344
primary cell
92
cell line
Organ
874
pancreas
705
liver
639
connective tissue
515
epithelium
460
adipose tissue
387
heart
230
vasculature
224
blood vessel
212
kidney
168
brain
159
bone element
135
artery
122
limb
81
musculature of body
69
blood
69
bodily fluid
61
eye
43
nerve
37
embryo
25
spleen
22
vein
20
lung
18
ureter
16
skeleton
5
gonad
5
ovary
2
intestine
2
pericardium
2
thymus
1
adrenal gland
1
bone marrow
1
esophagus
1
large intestine
1
lymph node
1
mammary gland
1
pituitary gland
1
skin of body
1
small intestine
1
spinal cord
1
stomach
1
urinary bladder
Project
688
AMP
152
HPAP
34
T1D
Genome assembly (visualization)
602
hg19
585
GRCh38
Lab
653
AMP-T2D consortium
152
Klaus Kaestner, Upenn
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:
81
inconsistent ontology term
4
audit script error
Audit category:
54
missing controlled_by
Audit category:
8
inconsistent control read length
1
inconsistent assembly
files.file_type!
tagAlign
month_released!
October, 2018
lab.title!
Katalin Susztak, Upenn
BIOSAMPLE
ASSAY
874 results
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total RNA-seq
ATAC-seq
ChIP-seq
single cell RNA-seq
WGBS
snATAC-seq
MeRIP-seq
Hi-C
DNase-seq
Capture-C
FAIRE-seq
RRBS
small RNA-seq
CRISPR genome editing followed by sgRNA sequencing
pCHi-C
tissue
islet of Langerhans
284
58
41
7
4
3
1
1
1
pancreas
2
7
2
4
1
2
1
1
1
body of pancreas
3
4
2
2
4
2
primary cell
pancreatic alpha cell
52
35
13
12
31
1
pancreatic beta cell
21
23
13
12
16
1
pancreatic acinar cell
2
9
8
12
1
pancreatic ductal cell
4
4
13
10
pancreatic endocrine cell
23
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cell line
EndoC_BH1
33
19
15
6
1
2
1
Panc1
13
1
1
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