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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
395
ChIP-seq
113
total RNA-seq
28
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
395
DNA binding
115
Transcription
30
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
recombinant protein
83
control
65
RNA binding protein
38
histone
38
histone modification
30
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
249
November, 2017
95
February, 2021
45
November, 2018
44
August, 2021
28
December, 2018
23
January, 2019
23
October, 2019
21
May, 2021
16
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
492
bam
434
bigWig
345
fastq
315
bed narrowPeak
274
bigBed narrowPeak
119
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
568
Homo sapiens
Biosample type
2771
tissue
1086
primary cell
572
cell line
394
in vitro differentiated cells
10
stem cell
Organ
318
liver
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
12
kidney
8
embryo
1
mammary gland
Project
561
AMP
9
T1D
2
community
Genome assembly (visualization)
444
hg19
375
GRCh38
Lab
525
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
85
inconsistent ontology term
1
inconsistent control
inconsistent replicate
Audit category:
12
missing controlled_by
Audit category:
25
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
audit.ERROR.category!
inconsistent replicate
files.file_type!
csv
target.investigated_as!
recombinant protein
BIOSAMPLE
ASSAY
572 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
296
14
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
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