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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
451
ChIP-seq
77
total RNA-seq
10
ATAC-seq
4
STARR-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-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
451
DNA binding
79
Transcription
12
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
345
transcription factor
82
recombinant protein
75
control
61
RNA binding protein
26
histone
26
histone modification
22
chromatin remodeller
13
broad histone mark
13
narrow histone mark
2
other context
2
other post-translational modification
Date released
311
November, 2017
70
February, 2021
57
November, 2018
41
August, 2021
28
December, 2018
23
January, 2019
17
October, 2019
6
February, 2023
4
March, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
512
bam
456
bigWig
419
fastq
375
bed narrowPeak
347
bigBed narrowPeak
80
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
1
vcf
Organism
558
Homo sapiens
Biosample type
2646
tissue
1033
primary cell
562
cell line
279
in vitro differentiated cells
9
stem cell
Organ
393
liver
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
16
pancreas
8
embryo
4
kidney
3
epithelium
1
mammary gland
Project
555
AMP
5
T1D
2
community
Genome assembly (visualization)
462
hg19
401
GRCh38
Lab
522
AMP-T2D consortium
33
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
7
missing controlled_by
Audit category:
26
inconsistent control read length
inconsistent control run_type
1
inconsistent assembly
audit.WARNING.category!
inconsistent control run_type
audit.ERROR.category!
inconsistent ontology term
BIOSAMPLE
ASSAY
562 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-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
370
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
H1-hESC
8
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