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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
1218
ChIP-seq
1055
total RNA-seq
287
ATAC-seq
180
single cell RNA-seq
178
DNase-seq
87
RNA microarray
pCHi-C
28
snATAC-seq
20
Hi-C
19
WGBS
16
small RNA-seq
10
MeRIP-seq
6
RRBS
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
FAIRE-seq
3
snDrop-seq
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
1255
Transcription
1218
DNA binding
496
DNA accessibility
25
DNA methylation
20
3D chromatin structure
1
DNA sequencing
Target of assay
544
histone
544
histone modification
432
transcription factor
294
narrow histone mark
250
broad histone mark
242
control
91
RNA binding protein
89
recombinant protein
32
chromatin remodeller
5
nucleotide modification
5
other context
5
other post-translational modification
Date released
640
February, 2021
397
November, 2017
August, 2017
273
August, 2021
268
October, 2019
193
May, 2020
163
June, 2019
120
July, 2018
115
May, 2019
101
February, 2023
87
November, 2018
80
April, 2019
77
July, 2019
74
October, 2018
66
May, 2022
60
May, 2021
56
November, 2019
51
December, 2017
47
September, 2023
40
May, 2024
35
December, 2018
30
January, 2019
27
March, 2020
25
February, 2020
23
October, 2017
19
April, 2020
15
May, 2023
10
November, 2020
8
January, 2021
6
April, 2018
6
September, 2017
5
March, 2019
4
January, 2018
4
March, 2023
3
December, 2019
1
August, 2022
1
October, 2022
Available data
2322
bam
2119
bigWig
1324
bed narrowPeak
1081
tsv
894
bigBed narrowPeak
633
fastq
246
bed broadPeak
235
bigBed broadPeak
199
tagAlign
184
bed bed3+
158
txt
64
xls
21
bed bedMethyl
21
bigBed bedMethyl
13
hic
12
bedpe bed3+
6
bed bed3
6
csv
3
tar
1
bedpe
1
hdf5
1
tagAlign bed3+
1
vcf
Organism
3122
Homo sapiens
Biosample type
2468
tissue
primary cell
656
cell line
in vitro differentiated cells
6
stem cell
Organ
705
liver
489
connective tissue
449
pancreas
430
adipose tissue
376
heart
316
kidney
263
brain
198
blood vessel
198
vasculature
158
bone element
139
artery
122
limb
94
epithelium
61
blood
61
bodily fluid
55
musculature of body
52
eye
43
nerve
24
spleen
19
lung
18
ureter
16
skeleton
8
embryo
4
gonad
4
ovary
2
pituitary gland
1
lymph node
1
pericardium
1
skin of body
1
spinal cord
Project
3021
AMP
47
KPMP
39
T1D
19
LungMap
4
community
Genome assembly (visualization)
2168
GRCh38
2107
hg19
1
hg18
Lab
2730
AMP-T2D consortium
142
Katalin Susztak, Upenn
56
Kyle Gaulton, UCSD
47
KPMP
40
Karen Mohlke, UNC
40
Patrick T. Ellinor, Broad
38
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:
179
inconsistent ontology term
28
inconsistent control
9
audit script error
1
inconsistent replicate
Audit category:
17
missing controlled_by
Audit category:
29
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_title!
pCHi-C
biosample_type!
in vitro differentiated cells
primary cell
month_released!
August, 2017
August, 2020
BIOSAMPLE
ASSAY
3130 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-seq
single cell RNA-seq
DNase-seq
RNA microarray
snATAC-seq
Hi-C
WGBS
small RNA-seq
MeRIP-seq
RRBS
STARR-seq
CRISPR genome editing followed by DNA sequencing
FAIRE-seq
snDrop-seq
Capture-C
HiChIP
CRISPR RNA-seq
CRISPR genome editing followed by sgRNA sequencing
...and 6 more
tissue
adipose tissue
382
3
islet of Langerhans
29
203
68
6
7
3
4
1
liver
97
167
20
1
2
1
1
kidney
27
49
75
64
13
6
1
1
1
bone element
84
+ See 165 more…
cell line
HepG2
378
14
1
2
1
2
EndoC_BH1
15
33
19
1
6
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
+ See 11 more…
stem cell
hESC
3
SB Ad3.1
1
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