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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
80
total RNA-seq
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
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
456
DNA binding
82
Transcription
2
3D chromatin structure
1
DNA accessibility
1
DNA methylation
1
DNA sequencing
Target of assay
360
transcription factor
89
recombinant protein
72
control
64
RNA binding protein
30
chromatin remodeller
19
histone
19
histone modification
10
narrow histone mark
9
broad histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
February, 2021
61
November, 2018
42
August, 2021
28
December, 2018
23
January, 2019
15
October, 2019
6
March, 2020
5
February, 2023
2
March, 2023
1
May, 2020
1
October, 2022
Available data
510
bam
465
bigWig
427
fastq
374
bed narrowPeak
348
bigBed narrowPeak
85
tsv
58
bed broadPeak
58
bigBed broadPeak
20
tagAlign
3
tar
1
bed bed3+
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hic
1
txt
1
vcf
Organism
557
Homo sapiens
Biosample type
2074
tissue
573
primary cell
560
cell line
349
in vitro differentiated cells
10
stem cell
Organ
400
liver
pancreas
60
blood
60
bodily fluid
60
epithelium
58
artery
58
blood vessel
58
heart
58
vasculature
19
kidney
8
embryo
1
mammary gland
Project
553
AMP
5
T1D
2
community
Genome assembly (visualization)
462
hg19
400
GRCh38
Lab
519
AMP-T2D consortium
34
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
16
inconsistent ontology term
1
inconsistent control
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
assay_title!
ATAC-seq
month_released!
September, 2020
organ_slims!
pancreas
BIOSAMPLE
ASSAY
560 results
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ChIP-seq
total RNA-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
378
14
2
2
2
1
1
GM12878
60
smooth muscle cell of the coronary artery
6
52
H1-hESC
8
EndoC_BH1
3
2
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