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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
440
ChIP-seq
61
total RNA-seq
21
ATAC-seq
6
MeRIP-seq
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
440
DNA binding
63
Transcription
23
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
357
transcription factor
89
recombinant protein
81
control
65
RNA binding protein
38
histone
histone modification
30
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
300
November, 2017
61
November, 2018
41
August, 2021
29
February, 2021
28
December, 2018
23
October, 2019
22
January, 2019
20
May, 2021
6
February, 2023
6
March, 2020
6
November, 2019
6
November, 2020
2
March, 2023
1
January, 2018
1
October, 2022
Available data
481
bam
429
bigWig
411
fastq
357
bed narrowPeak
335
bigBed narrowPeak
62
tsv
45
bed broadPeak
45
bigBed broadPeak
3
tagAlign
3
tar
2
bed bed3+
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
548
Homo sapiens
Biosample type
2046
tissue
819
primary cell
552
cell line
277
in vitro differentiated cells
4
stem cell
Organ
381
liver
73
pancreas
67
epithelium
66
artery
blood vessel
66
heart
66
vasculature
60
blood
60
bodily fluid
17
kidney
8
embryo
Project
543
AMP
7
T1D
2
community
Genome assembly (visualization)
428
hg19
368
GRCh38
Lab
508
AMP-T2D consortium
31
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
78
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
12
missing controlled_by
Audit category:
15
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
target.investigated_as!
histone modification
organ_slims!
blood vessel
assay_title!
pCHi-C
BIOSAMPLE
ASSAY
552 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
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
360
14
1
2
2
1
1
EndoC_BH1
3
33
19
6
1
3
2
2
1
GM12878
59
1
H1-hESC
8
Panc1
6
1
1
RCC 7860 HIF1a re-expression
4
1
RCC 7860 HIF2a over-expression
3
1
RCC 7860 vector
3
1
EndoC-BH1
1
1
HEK293T
2
early embryonic cell
2
glomerular visceral epithelial cell
1
1
iPSC derived cell line
2
MIN6
1
Synthesized DNA
1
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