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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
450
ChIP-seq
62
total RNA-seq
10
ATAC-seq
6
pCHi-C
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
Assay category
450
DNA binding
64
Transcription
11
DNA accessibility
2
3D chromatin structure
1
DNA methylation
Target of assay
348
transcription factor
89
recombinant protein
74
control
63
RNA binding protein
29
chromatin remodeller
23
histone
23
histone modification
12
broad histone mark
11
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
70
February, 2021
61
November, 2018
August, 2021
28
October, 2019
27
December, 2018
23
January, 2019
6
March, 2020
5
February, 2023
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
522
bam
449
bigWig
426
fastq
374
bed narrowPeak
353
bigBed narrowPeak
67
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
Organism
537
Homo sapiens
Biosample type
2506
tissue
682
primary cell
540
cell line
328
in vitro differentiated cells
10
stem cell
Organ
370
liver
90
pancreas
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
60
blood
60
bodily fluid
17
kidney
1
mammary gland
Project
533
AMP
5
T1D
2
community
Genome assembly (visualization)
454
hg19
406
GRCh38
Lab
533
AMP-T2D consortium
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
15
inconsistent ontology term
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
audit.ERROR.category!
inconsistent control
organ_slims!
epithelium
month_released!
August, 2021
BIOSAMPLE
ASSAY
540 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
HiChIP
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
360
5
1
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
59
1
Panc1
13
1
1
EndoC_BH1
3
2
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