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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
338
ChIP-seq
80
total RNA-seq
10
ATAC-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
2
Hi-C
2
HiChIP
1
DNase-seq
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
338
DNA binding
82
Transcription
11
DNA accessibility
2
3D chromatin structure
1
DNA sequencing
Target of assay
259
transcription factor
73
recombinant protein
69
control
39
RNA binding protein
19
chromatin remodeller
5
histone
5
histone modification
4
narrow histone mark
1
broad histone mark
1
other context
1
other post-translational modification
Date released
257
November, 2017
70
February, 2021
November, 2018
42
August, 2021
28
December, 2018
23
January, 2019
15
October, 2019
6
March, 2020
5
February, 2023
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
458
bam
409
bigWig
366
fastq
327
bed narrowPeak
292
bigBed narrowPeak
85
tsv
58
bed broadPeak
bigBed broadPeak
20
tagAlign
3
tar
1
bed bed3
1
bed bed3+
1
bedpe bed3+
1
hic
1
txt
1
vcf
Organism
448
Homo sapiens
Biosample type
2090
tissue
692
primary cell
451
cell line
390
in vitro differentiated cells
10
stem cell
Organ
297
liver
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
46
blood
46
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
444
AMP
5
T1D
2
community
Genome assembly (visualization)
360
hg19
308
GRCh38
Lab
410
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:
10
missing controlled_by
Audit category:
8
inconsistent control read length
4
inconsistent control run_type
files.file_type!
bigBed broadPeak
organ_slims!
pancreas
month_released!
November, 2018
BIOSAMPLE
ASSAY
451 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
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
275
14
1
2
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
45
1
H1-hESC
8
EndoC_BH1
3
2
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