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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
1298
ChIP-seq
1100
total RNA-seq
261
ATAC-seq
180
single cell RNA-seq
144
DNase-seq
28
snATAC-seq
27
WGBS
27
pCHi-C
16
small RNA-seq
14
Hi-C
11
RRBS
4
FAIRE-seq
4
MeRIP-seq
4
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
RNA microarray
3
snDrop-seq
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
1298
DNA binding
1298
Transcription
437
DNA accessibility
38
DNA methylation
14
3D chromatin structure
1
DNA sequencing
Target of assay
603
histone modification
602
histone
447
transcription factor
320
narrow histone mark
282
broad histone mark
245
control
92
RNA binding protein
82
recombinant protein
32
chromatin remodeller
5
other context
5
other post-translational modification
2
nucleotide modification
Date released
525
February, 2021
397
November, 2017
284
August, 2017
270
August, 2021
194
May, 2020
188
October, 2019
131
June, 2019
120
July, 2018
108
May, 2019
101
February, 2023
87
November, 2018
80
April, 2019
74
October, 2018
72
July, 2019
66
May, 2022
48
December, 2017
47
September, 2023
42
March, 2020
40
May, 2021
40
May, 2024
39
November, 2019
35
December, 2018
30
January, 2019
23
October, 2017
21
February, 2020
19
April, 2020
15
May, 2023
8
January, 2021
6
April, 2018
6
September, 2017
4
March, 2019
4
November, 2020
3
December, 2019
3
January, 2018
2
March, 2023
1
August, 2022
1
October, 2022
Available data
2310
bam
2143
bigWig
1272
bed narrowPeak
1146
tsv
832
bigBed narrowPeak
804
fastq
258
tagAlign
236
bed broadPeak
199
bigBed broadPeak
172
bed bed3+
74
txt
64
xls
25
bed bedMethyl
25
bigBed bedMethyl
12
hic
11
bedpe bed3+
6
bed bed3
6
csv
3
tar
bedpe
1
hdf5
1
tagAlign bed3+
1
vcf
Organism
3121
Homo sapiens
Biosample type
2564
tissue
1034
primary cell
570
cell line
279
in vitro differentiated cells
9
stem cell
Organ
762
liver
546
connective tissue
520
pancreas
487
adipose tissue
379
heart
303
kidney
262
brain
199
blood vessel
199
vasculature
139
artery
limb
81
musculature of body
74
bone element
61
blood
61
bodily fluid
56
eye
43
nerve
25
spleen
20
lung
18
epithelium
18
ureter
16
skeleton
8
embryo
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
1
pericardium
1
skin of body
1
small intestine
1
spinal cord
Project
3030
AMP
47
KPMP
36
T1D
19
LungMap
2
community
Genome assembly (visualization)
2167
GRCh38
2125
hg19
Lab
2743
AMP-T2D consortium
142
Katalin Susztak, Upenn
57
Kyle Gaulton, UCSD
47
KPMP
40
Karen Mohlke, UNC
40
Patrick T. Ellinor, Broad
36
Bing Ren, UCSD
19
Xin Sun, UCSD
4
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
2
Mark McCarthy, Oxford
1
Maike Sander, UCSD
1
Stephen Parker, UMich
Audit category:
inconsistent ontology term
28
inconsistent control
9
audit script error
1
inconsistent replicate
Audit category:
39
missing controlled_by
Audit category:
32
inconsistent control read length
8
inconsistent control run_type
2
inconsistent assembly
audit.ERROR.category!
inconsistent ontology term
files.file_type!
bedpe
organ_slims!
limb
BIOSAMPLE
ASSAY
3134 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-seq
single cell RNA-seq
DNase-seq
snATAC-seq
WGBS
pCHi-C
small RNA-seq
Hi-C
RRBS
FAIRE-seq
MeRIP-seq
STARR-seq
CRISPR genome editing followed by DNA sequencing
RNA microarray
snDrop-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
...and 3 more
tissue
islet of Langerhans
70
292
68
6
1
7
4
2
1
1
4
adipose tissue
2
382
3
3
1
liver
145
167
20
1
2
3
1
1
1
1
kidney
27
49
75
64
13
6
1
1
1
heart left ventricle
35
3
2
18
3
4
1
1
1
+ See 157 more…
cell line
HepG2
378
14
1
1
2
2
2
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
H1-hESC
8
+ See 9 more…
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