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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
443
ChIP-seq
79
total RNA-seq
10
ATAC-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
HiChIP
1
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
443
DNA binding
81
Transcription
11
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
345
transcription factor
88
recombinant protein
78
control
58
RNA binding protein
19
chromatin remodeller
15
histone
15
histone modification
8
narrow histone mark
7
broad histone mark
2
other context
2
other post-translational modification
Date released
294
November, 2017
70
February, 2021
56
November, 2018
42
August, 2021
28
December, 2018
28
October, 2019
23
January, 2019
6
March, 2020
5
February, 2023
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
505
bam
446
bigWig
401
fastq
365
bed narrowPeak
330
bigBed narrowPeak
84
tsv
46
bed broadPeak
46
bigBed broadPeak
9
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
554
Homo sapiens
Biosample type
2716
tissue
679
primary cell
557
cell line
354
in vitro differentiated cells
8
stem cell
Organ
375
liver
92
pancreas
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
550
AMP
5
T1D
2
community
Genome assembly (visualization)
452
hg19
393
GRCh38
Lab
516
AMP-T2D consortium
34
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
16
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
8
missing controlled_by
Audit category:
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
month_released!
June, 2018
organ_slims!
epithelium
audit.WARNING.category!
inconsistent control read length
BIOSAMPLE
ASSAY
557 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
HiChIP
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
352
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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