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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
459
ChIP-seq
109
total RNA-seq
29
ATAC-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
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
459
DNA binding
111
Transcription
29
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
354
transcription factor
82
recombinant protein
74
control
65
RNA binding protein
31
histone
31
histone modification
30
chromatin remodeller
16
narrow histone mark
15
broad histone mark
3
nucleotide modification
other context
2
other post-translational modification
Date released
313
November, 2017
96
February, 2021
61
November, 2018
44
August, 2021
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
551
bam
500
bigWig
425
fastq
387
bed narrowPeak
345
bigBed narrowPeak
115
tsv
57
bed broadPeak
57
bigBed broadPeak
20
tagAlign
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bed3+
1
bed bedMethyl
1
bigBed bedMethyl
1
txt
1
vcf
Organism
626
Homo sapiens
Biosample type
2532
tissue
1054
primary cell
630
cell line
386
in vitro differentiated cells
9
stem cell
Organ
399
liver
77
epithelium
77
pancreas
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
8
embryo
4
kidney
1
mammary gland
Project
619
AMP
9
T1D
2
community
Genome assembly (visualization)
508
hg19
442
GRCh38
Lab
583
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:
79
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
assay_title!
CRISPR RNA-seq
month_released!
October, 2019
target.investigated_as!
other context
BIOSAMPLE
ASSAY
630 results
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ChIP-seq
total RNA-seq
ATAC-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
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
376
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
3
1
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
H1-hESC
8
EndoC-BH1
1
1
HEK293T
2
early embryonic cell
2
iPSC derived cell line
2
MCF-7
1
MIN6
1
RCC 7860 VHL
1
RCC 7860 vector
1
Synthesized DNA
1
fibroblast cell line
1
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