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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
431
ChIP-seq
113
total RNA-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
431
DNA binding
115
Transcription
DNA accessibility
3
3D chromatin structure
1
DNA sequencing
Target of assay
321
transcription factor
88
recombinant protein
83
control
57
RNA binding protein
27
histone
27
histone modification
17
chromatin remodeller
14
narrow histone mark
13
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
294
November, 2017
87
February, 2021
55
November, 2018
44
August, 2021
December, 2018
28
October, 2019
23
January, 2019
15
November, 2019
9
March, 2020
6
February, 2023
6
November, 2020
5
May, 2021
2
March, 2023
1
May, 2020
1
October, 2022
Available data
517
bam
464
bigWig
373
fastq
341
bed narrowPeak
302
bigBed narrowPeak
118
tsv
45
bed broadPeak
45
bigBed broadPeak
9
tagAlign
3
tar
2
bed bed3+
2
bedpe bed3+
2
hic
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
572
Homo sapiens
Biosample type
2269
tissue
785
primary cell
576
cell line
334
in vitro differentiated cells
8
stem cell
Organ
372
liver
72
pancreas
59
epithelium
58
artery
58
blood vessel
58
heart
58
vasculature
33
blood
33
bodily fluid
18
kidney
8
embryo
1
mammary gland
Project
565
AMP
9
T1D
2
community
Genome assembly (visualization)
462
hg19
402
GRCh38
Lab
529
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
73
inconsistent ontology term
Audit category:
8
missing controlled_by
Audit category:
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_slims!
DNA accessibility
audit.WARNING.category!
inconsistent control read length
files.file_type!
bed bedMethyl
month_released!
December, 2018
BIOSAMPLE
ASSAY
576 results
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ChIP-seq
total RNA-seq
MeRIP-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
352
14
2
2
1
1
EndoC_BH1
15
33
6
3
1
2
2
1
smooth muscle cell of the coronary artery
6
52
GM12878
33
Panc1
13
1
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