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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
1265
ChIP-seq
220
ATAC-seq
153
DNase-seq
86
total RNA-seq
85
RNA microarray
70
single cell RNA-seq
28
snATAC-seq
20
WGBS
17
Hi-C
10
MeRIP-seq
10
RRBS
6
pCHi-C
5
STARR-seq
4
FAIRE-seq
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
HiChIP
1
CRISPR RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
CRISPRi RNA-seq
1
GRO-seq
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
1265
DNA binding
405
DNA accessibility
160
Transcription
30
DNA methylation
17
3D chromatin structure
1
DNA sequencing
Target of assay
573
histone modification
572
histone
439
transcription factor
306
narrow histone mark
266
broad histone mark
253
control
89
recombinant protein
83
RNA binding protein
32
chromatin remodeller
5
nucleotide modification
5
other context
5
other post-translational modification
Date released
397
November, 2017
254
October, 2019
195
August, 2017
157
August, 2021
136
June, 2019
97
February, 2021
94
May, 2019
87
November, 2018
74
October, 2018
61
February, 2023
51
December, 2017
50
May, 2020
47
September, 2023
36
November, 2019
35
December, 2018
26
May, 2022
25
January, 2019
23
April, 2019
23
October, 2017
19
April, 2020
19
May, 2021
17
July, 2019
15
May, 2023
12
March, 2020
10
November, 2020
8
January, 2021
6
September, 2017
5
March, 2019
4
January, 2018
4
July, 2018
4
March, 2023
1
August, 2022
1
December, 2019
1
October, 2022
Available data
2294
bam
2064
bigWig
1185
bed narrowPeak
tsv
828
bigBed narrowPeak
808
fastq
252
tagAlign
245
bed broadPeak
208
bigBed broadPeak
184
bed bed3+
158
txt
64
xls
19
bed bedMethyl
19
bigBed bedMethyl
10
hic
9
bedpe bed3+
6
bed bed3
6
csv
3
tar
1
bedpe
1
hdf5
1
tagAlign bed3+
1
vcf
Organism
1979
Homo sapiens
Biosample type
1459
tissue
primary cell
529
cell line
in vitro differentiated cells
6
stem cell
Organ
553
liver
300
kidney
288
pancreas
242
brain
heart
133
blood vessel
133
vasculature
115
limb
100
bone element
90
connective tissue
89
adipose tissue
83
artery
75
musculature of body
61
blood
61
bodily fluid
56
epithelium
51
eye
38
nerve
24
spleen
19
lung
18
ureter
16
skeleton
4
gonad
4
ovary
2
pituitary gland
1
lymph node
1
pericardium
1
skin of body
1
thymus
Project
1886
AMP
47
KPMP
38
T1D
19
LungMap
4
community
Genome assembly (visualization)
1133
hg19
1115
GRCh38
1
hg18
Lab
1683
AMP-T2D consortium
142
Katalin Susztak, Upenn
57
Kyle Gaulton, UCSD
47
KPMP
Karen Mohlke, UNC
28
Bing Ren, UCSD
19
Xin Sun, UCSD
10
Rohit N. Kulkarni, M.D., Ph.D.
4
Anna Gloyn, Oxford
2
Mark McCarthy, Oxford
1
Maike Sander, UCSD
1
Stephen Parker, UMich
Audit category:
141
inconsistent ontology term
28
inconsistent control
2
audit script error
1
inconsistent replicate
Audit category:
39
missing controlled_by
Audit category:
34
inconsistent control read length
8
inconsistent control run_type
2
inconsistent assembly
biosample_type!
in vitro differentiated cells
primary cell
files.file_type!
tsv
lab.title!
Karen Mohlke, UNC
organ_slims!
heart
BIOSAMPLE
ASSAY
1994 results
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Clear Filters
ChIP-seq
ATAC-seq
DNase-seq
total RNA-seq
RNA microarray
single cell RNA-seq
snATAC-seq
WGBS
Hi-C
MeRIP-seq
RRBS
pCHi-C
STARR-seq
FAIRE-seq
CRISPR genome editing followed by DNA sequencing
Capture-C
HiChIP
CRISPR RNA-seq
CRISPR genome editing followed by sgRNA sequencing
CRISPRi RNA-seq
...and 5 more
tissue
kidney
27
75
13
49
59
6
1
1
1
islet of Langerhans
71
67
1
31
7
3
4
1
4
1
liver
145
2
1
3
1
1
bone element
84
body of pancreas
35
4
4
2
+ See 138 more…
cell line
HepG2
378
1
1
2
1
2
GM12878
60
1
EndoC_BH1
15
18
1
6
3
2
2
1
Panc1
13
1
1
RCC 7860 HIF1a re-expression
4
+ See 8 more…
stem cell
hESC
3
SB Ad3.1
1
1
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