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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
763
ChIP-seq
total RNA-seq
227
ATAC-seq
187
single cell RNA-seq
56
snATAC-seq
48
WGBS
33
DNase-seq
23
pCHi-C
14
Hi-C
10
RRBS
6
MeRIP-seq
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
HiChIP
2
small RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
DNAme array
1
FAIRE-seq
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
763
DNA binding
317
DNA accessibility
191
Transcription
59
DNA methylation
14
3D chromatin structure
1
DNA sequencing
Target of assay
371
transcription factor
275
histone
275
histone modification
141
broad histone mark
134
narrow histone mark
118
control
89
recombinant protein
75
RNA binding protein
31
chromatin remodeller
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
324
November, 2017
168
May, 2021
134
May, 2022
101
May, 2020
63
February, 2021
62
November, 2018
59
August, 2017
58
October, 2019
55
June, 2019
48
July, 2018
47
September, 2018
43
April, 2018
43
September, 2020
31
August, 2021
28
December, 2018
18
February, 2023
18
January, 2019
18
July, 2019
15
November, 2019
8
January, 2021
8
March, 2020
8
November, 2020
7
August, 2020
5
May, 2019
5
September, 2017
4
October, 2022
3
August, 2018
3
June, 2018
3
March, 2023
1
January, 2018
Available data
937
bam
879
bigWig
711
fastq
699
bed narrowPeak
464
bigBed narrowPeak
153
zippedFastqFolder
126
tsv
120
tagAlign
108
bed broadPeak
108
bigBed broadPeak
38
bed bed3+
11
bed bedMethyl
11
bigBed bedMethyl
8
hic
6
bedpe bed3+
5
hdf5
4
tar
3
cool
bed bed3
2
csv
1
txt
1
vcf
Organism
1384
Homo sapiens
Biosample type
1648
tissue
840
primary cell
548
cell line
253
in vitro differentiated cells
10
stem cell
Organ
395
liver
358
epithelium
324
pancreas
69
blood
69
bodily fluid
49
vasculature
45
kidney
43
blood vessel
28
connective tissue
23
heart
22
vein
21
brain
14
artery
13
musculature of body
5
eye
1
adipose tissue
1
bone element
1
bone marrow
1
mammary gland
Project
1038
AMP
232
HPAP
115
T1D
2
community
1
ITG
Genome assembly (visualization)
900
hg19
744
GRCh38
Lab
976
AMP-T2D consortium
232
Klaus Kaestner, Upenn
146
Kyle Gaulton, UCSD
25
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
1
ITG
Audit category:
106
inconsistent ontology term
31
audit script error
1
inconsistent control
Audit category:
57
missing controlled_by
Audit category:
31
inconsistent control read length
9
inconsistent control run_type
3
inconsistent assembly
assay_title!
total RNA-seq
files.file_type!
bed bed3
lab.title!
Katalin Susztak, Upenn
BIOSAMPLE
ASSAY
1388 results
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Clear Filters
ChIP-seq
ATAC-seq
single cell RNA-seq
snATAC-seq
WGBS
DNase-seq
pCHi-C
Hi-C
RRBS
MeRIP-seq
STARR-seq
CRISPR genome editing followed by DNA sequencing
Capture-C
HiChIP
small RNA-seq
CRISPR genome editing followed by sgRNA sequencing
DNAme array
FAIRE-seq
MPRA
shRNA RNA-seq
...and 2 more
primary cell
Langerhans cell
85
48
monocyte
85
15
1
1
pancreatic alpha cell
13
35
12
31
1
pancreatic beta cell
13
23
12
16
1
CD8-positive, alpha-beta T cell
33
2
1
+ See 86 more…
cell line
HepG2
378
1
2
2
2
GM12878
60
1
EndoC_BH1
15
19
1
6
3
2
2
1
Panc1
13
1
1
smooth muscle cell of the coronary artery
6
8
+ See 12 more…
See all biosamples
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