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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
458
ChIP-seq
113
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
458
DNA binding
115
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
346
transcription factor
88
recombinant protein
83
control
59
RNA binding protein
27
histone
27
histone modification
19
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
96
February, 2021
56
November, 2018
44
August, 2021
30
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
556
bam
496
bigWig
401
fastq
380
bed narrowPeak
331
bigBed narrowPeak
119
tsv
46
bed broadPeak
46
bigBed broadPeak
9
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
632
Homo sapiens
Biosample type
2765
tissue
1081
primary cell
636
cell line
377
in vitro differentiated cells
8
stem cell
Organ
375
liver
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
625
AMP
9
T1D
2
community
Genome assembly (visualization)
504
hg19
442
GRCh38
Lab
589
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:
92
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
8
missing controlled_by
Audit category:
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
audit.WARNING.category!
inconsistent control read length
files.file_type!
csv
BIOSAMPLE
ASSAY
636 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
352
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
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