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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
456
ChIP-seq
79
total RNA-seq
10
ATAC-seq
6
pCHi-C
5
STARR-seq
3
Hi-C
1
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
456
DNA binding
81
Transcription
11
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
348
transcription factor
88
recombinant protein
78
control
62
RNA binding protein
25
histone
25
histone modification
24
chromatin remodeller
13
broad histone mark
12
narrow histone mark
2
other context
2
other post-translational modification
Date released
305
November, 2017
70
February, 2021
58
November, 2018
42
August, 2021
28
December, 2018
28
October, 2019
23
January, 2019
6
March, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
518
bam
460
bigWig
414
fastq
377
bed narrowPeak
342
bigBed narrowPeak
84
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
562
Homo sapiens
Biosample type
2683
tissue
565
cell line
420
primary cell
317
in vitro differentiated cells
10
stem cell
Organ
388
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
563
AMP
2
community
Genome assembly (visualization)
466
hg19
410
GRCh38
Lab
529
AMP-T2D consortium
34
Bing Ren, UCSD
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
16
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
missing controlled_by
Audit category:
21
inconsistent control read length
2
inconsistent control run_type
1
inconsistent assembly
audit.NOT_COMPLIANT.category!
missing controlled_by
lab.title!
Kyle Gaulton, UCSD
organ_slims!
epithelium
esophagus
BIOSAMPLE
ASSAY
565 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
STARR-seq
Hi-C
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
365
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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