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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
409
ChIP-seq
77
total RNA-seq
10
ATAC-seq
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
HiChIP
2
pCHi-C
1
DNase-seq
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
409
DNA binding
79
Transcription
11
DNA accessibility
3
3D chromatin structure
1
DNA sequencing
Target of assay
303
transcription factor
75
control
73
recombinant protein
43
RNA binding protein
26
histone
26
histone modification
23
chromatin remodeller
13
broad histone mark
13
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
70
February, 2021
November, 2018
42
August, 2021
28
December, 2018
28
October, 2019
23
January, 2019
March, 2020
5
February, 2023
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
468
bam
413
bigWig
366
fastq
333
bed narrowPeak
298
bigBed narrowPeak
78
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bedpe bed3+
1
hdf5
1
hic
1
txt
1
vcf
Organism
513
Homo sapiens
Biosample type
2610
tissue
681
primary cell
516
cell line
362
in vitro differentiated cells
6
stem cell
Organ
355
liver
87
pancreas
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
46
blood
46
bodily fluid
17
kidney
8
embryo
Project
509
AMP
5
T1D
2
community
Genome assembly (visualization)
422
hg19
356
GRCh38
Lab
475
AMP-T2D consortium
34
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
14
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
10
missing controlled_by
Audit category:
21
inconsistent control read length
4
inconsistent control run_type
1
inconsistent assembly
assay_title!
RNA microarray
month_released!
March, 2020
November, 2018
organ_slims!
epithelium
BIOSAMPLE
ASSAY
516 results
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ChIP-seq
total RNA-seq
ATAC-seq
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
HiChIP
pCHi-C
DNase-seq
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
333
14
1
2
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
45
1
Panc1
13
1
1
H1-hESC
8
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