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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
406
ChIP-seq
113
total RNA-seq
29
ATAC-seq
10
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
3
MeRIP-seq
2
Capture-C
2
DNase-seq
2
HiChIP
1
CRISPR RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
CRISPRi RNA-seq
1
GRO-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
406
DNA binding
117
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
89
recombinant protein
control
65
RNA binding protein
40
histone
40
histone modification
30
chromatin remodeller
20
broad histone mark
20
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
259
November, 2017
93
February, 2021
58
November, 2018
40
August, 2021
28
December, 2018
21
May, 2021
21
October, 2019
20
January, 2019
15
March, 2020
14
November, 2019
6
February, 2023
4
March, 2023
3
November, 2020
2
December, 2017
2
January, 2018
1
May, 2020
1
October, 2022
Available data
512
bigWig
508
bam
406
bed narrowPeak
368
fastq
355
bigBed narrowPeak
123
tsv
59
bed broadPeak
59
bigBed broadPeak
16
tagAlign
5
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
582
Homo sapiens
Biosample type
tissue
1053
primary cell
579
cell line
357
in vitro differentiated cells
9
stem cell
Organ
341
liver
81
pancreas
74
epithelium
64
artery
64
blood vessel
64
heart
64
vasculature
55
blood
55
bodily fluid
16
kidney
8
embryo
1
connective tissue
1
mammary gland
Project
575
AMP
9
T1D
4
community
Genome assembly (visualization)
519
hg19
466
GRCh38
1
hg18
Lab
546
AMP-T2D consortium
30
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
4
Anna Gloyn, Oxford
3
Rohit N. Kulkarni, M.D., Ph.D.
Audit category:
85
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
28
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
biosample_type!
tissue
organ_slims!
limb
target.investigated_as!
control
BIOSAMPLE
ASSAY
588 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
MeRIP-seq
Capture-C
DNase-seq
HiChIP
CRISPR RNA-seq
CRISPR genome editing followed by sgRNA sequencing
CRISPRi RNA-seq
GRO-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
318
14
1
2
2
2
1
1
EndoC_BH1
13
33
19
1
3
3
2
2
1
smooth muscle cell of the coronary artery
4
52
8
GM12878
54
1
Panc1
7
1
1
+ See 14 more…
stem cell
hESC
2
1
SB Ad3.1
1
1
mesenchymal stem cell
1
mesendoderm
1
neural progenitor cell (neural stem cell)
1
+ See 1 more…
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