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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
200
ChIP-seq
142
ATAC-seq
106
total RNA-seq
87
single cell RNA-seq
56
snATAC-seq
47
WGBS
20
pCHi-C
11
Hi-C
8
RRBS
4
DNase-seq
4
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
2
HiChIP
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
203
DNA accessibility
200
DNA binding
195
Transcription
56
DNA methylation
11
3D chromatin structure
1
DNA sequencing
Target of assay
102
control
53
transcription factor
45
histone
45
histone modification
29
broad histone mark
16
narrow histone mark
8
RNA binding protein
2
chromatin remodeller
1
recombinant protein
Date released
134
May, 2022
101
November, 2017
99
May, 2020
88
February, 2023
56
May, 2021
56
September, 2020
50
February, 2021
34
August, 2021
19
October, 2019
17
August, 2017
11
July, 2019
8
January, 2021
5
November, 2018
4
June, 2019
4
October, 2022
3
January, 2019
3
March, 2020
2
March, 2023
1
December, 2018
1
January, 2018
1
September, 2018
Available data
286
fastq
189
bam
156
bigWig
153
zippedFastqFolder
80
bed narrowPeak
36
bigBed narrowPeak
24
tsv
18
bed broadPeak
18
bigBed broadPeak
8
bed bed3+
8
bed bedMethyl
8
bigBed bedMethyl
8
tagAlign
6
hic
5
bedpe bed3+
4
hdf5
4
tar
3
cool
2
csv
1
txt
1
vcf
Organism
693
Homo sapiens
Biosample type
831
tissue
534
primary cell
163
cell line
113
in vitro differentiated cells
6
stem cell
Organ
179
epithelium
162
pancreas
136
liver
17
vasculature
15
blood
15
blood vessel
15
bodily fluid
10
vein
7
brain
7
kidney
4
connective tissue
3
heart
2
artery
2
eye
2
musculature of body
1
bone element
1
bone marrow
1
mammary gland
Project
353
AMP
314
HPAP
28
T1D
2
community
Genome assembly (visualization)
1054
hg19
GRCh38
Lab
314
Klaus Kaestner, Upenn
285
AMP-T2D consortium
63
Kyle Gaulton, UCSD
33
Bing Ren, UCSD
2
Anna Gloyn, Oxford
Audit category:
inconsistent ontology term
31
audit script error
Audit category:
8
missing controlled_by
Audit category:
4
inconsistent control read length
2
inconsistent control run_type
assembly!
GRCh38
audit.ERROR.category!
inconsistent ontology term
month_released!
June, 2018
BIOSAMPLE
ASSAY
697 results
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Clear Filters
ChIP-seq
ATAC-seq
total RNA-seq
single cell RNA-seq
snATAC-seq
WGBS
pCHi-C
Hi-C
RRBS
DNase-seq
STARR-seq
CRISPR genome editing followed by DNA sequencing
HiChIP
CRISPR genome editing followed by sgRNA sequencing
DNAme array
FAIRE-seq
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
primary cell
Langerhans cell
85
48
pancreatic alpha cell
6
22
42
31
1
pancreatic beta cell
6
13
11
16
1
exocrine cell
39
CD8-positive, alpha-beta T cell
33
2
2
1
+ See 56 more…
cell line
HepG2
117
9
2
2
2
1
GM12878
6
1
Panc1
7
EndoC_BH1
3
2
1
EndoC-BH1
1
1
+ See 6 more…
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