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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
470
ChIP-seq
113
total RNA-seq
29
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
470
DNA binding
115
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
348
transcription factor
88
recombinant protein
83
control
63
RNA binding protein
37
histone
37
histone modification
23
chromatin remodeller
19
broad histone mark
18
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
305
November, 2017
96
February, 2021
58
November, 2018
44
August, 2021
30
October, 2019
27
December, 2018
23
January, 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
568
bam
509
bigWig
413
fastq
391
bed narrowPeak
342
bigBed narrowPeak
119
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
644
Homo sapiens
Biosample type
2724
tissue
985
primary cell
648
cell line
388
in vitro differentiated cells
10
stem cell
Organ
388
liver
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
60
blood
60
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
637
AMP
9
T1D
2
community
Genome assembly (visualization)
517
hg19
458
GRCh38
Lab
601
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:
92
inconsistent ontology term
inconsistent control
1
inconsistent replicate
Audit category:
missing controlled_by
Audit category:
21
inconsistent control read length
2
inconsistent control run_type
1
inconsistent assembly
month_released!
September, 2020
audit.NOT_COMPLIANT.category!
missing controlled_by
audit.ERROR.category!
inconsistent control
BIOSAMPLE
ASSAY
648 results
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Clear Filters
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
365
14
1
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
59
1
Panc1
13
1
1
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