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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
454
ChIP-seq
109
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
4
Hi-C
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
STARR-seq
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
454
DNA binding
111
Transcription
30
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
349
transcription factor
82
recombinant protein
76
control
65
RNA binding protein
30
chromatin remodeller
27
histone
27
histone modification
14
narrow histone mark
13
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
303
November, 2017
88
February, 2021
61
November, 2018
42
August, 2021
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
15
October, 2019
9
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
567
bam
510
bigWig
427
fastq
396
bed narrowPeak
354
bigBed narrowPeak
113
tsv
59
bed broadPeak
59
bigBed broadPeak
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
619
Homo sapiens
Biosample type
2200
tissue
952
primary cell
623
cell line
354
in vitro differentiated cells
10
stem cell
Organ
389
liver
92
pancreas
79
epithelium
61
blood
61
bodily fluid
60
artery
60
blood vessel
60
heart
60
vasculature
kidney
8
embryo
1
mammary gland
Project
612
AMP
9
T1D
2
community
Genome assembly (visualization)
501
hg19
438
GRCh38
Lab
578
AMP-T2D consortium
32
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
77
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
15
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
organ_slims!
kidney
files.file_type!
tagAlign
BIOSAMPLE
ASSAY
623 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
Hi-C
pCHi-C
CRISPR genome editing followed by DNA sequencing
STARR-seq
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
366
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
GM12878
60
1
smooth muscle cell of the coronary artery
52
8
Panc1
13
1
1
H1-hESC
8
EndoC-BH1
1
1
early embryonic cell
2
MCF-7
1
MIN6
1
Synthesized DNA
1
fibroblast cell line
1
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