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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
446
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
446
DNA binding
79
Transcription
12
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
353
transcription factor
82
recombinant protein
75
control
64
RNA binding protein
30
chromatin remodeller
26
histone
26
histone modification
13
broad histone mark
narrow histone mark
2
other context
2
other post-translational modification
Date released
308
November, 2017
70
February, 2021
61
November, 2018
39
August, 2021
28
December, 2018
22
January, 2019
14
October, 2019
6
February, 2023
4
March, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
509
bam
451
bigWig
419
fastq
371
bed narrowPeak
345
bigBed narrowPeak
80
tsv
53
bed broadPeak
53
bigBed broadPeak
15
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
553
Homo sapiens
Biosample type
2339
tissue
928
primary cell
557
cell line
226
in vitro differentiated cells
8
stem cell
Organ
392
liver
66
artery
66
blood vessel
66
heart
66
vasculature
60
blood
60
bodily fluid
13
pancreas
8
embryo
4
kidney
3
epithelium
1
mammary gland
Project
550
AMP
5
T1D
2
community
Genome assembly (visualization)
457
hg19
397
GRCh38
Lab
519
AMP-T2D consortium
31
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
12
missing controlled_by
Audit category:
21
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
audit.ERROR.category!
inconsistent ontology term
target.investigated_as!
narrow histone mark
BIOSAMPLE
ASSAY
557 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
369
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
59
1
Panc1
10
1
1
H1-hESC
8
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