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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
457
ChIP-seq
77
total RNA-seq
10
ATAC-seq
4
STARR-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-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
457
DNA binding
79
Transcription
12
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
353
transcription factor
82
recombinant protein
75
control
64
RNA binding protein
30
chromatin remodeller
26
histone
26
histone modification
13
broad histone mark
13
narrow histone mark
other context
2
other post-translational modification
Date released
313
November, 2017
70
February, 2021
61
November, 2018
41
August, 2021
28
December, 2018
23
January, 2019
17
October, 2019
6
February, 2023
4
March, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
518
bam
462
bigWig
425
fastq
381
bed narrowPeak
353
bigBed narrowPeak
80
tsv
58
bed broadPeak
58
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
1
vcf
Organism
564
Homo sapiens
Biosample type
2619
tissue
1034
primary cell
568
cell line
279
in vitro differentiated cells
9
stem cell
Organ
399
liver
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
16
pancreas
8
embryo
4
kidney
3
epithelium
1
mammary gland
Project
561
AMP
5
T1D
2
community
Genome assembly (visualization)
468
hg19
405
GRCh38
Lab
528
AMP-T2D consortium
33
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
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
1
inconsistent assembly
audit.ERROR.category!
inconsistent ontology term
files.file_type!
xls
target.investigated_as!
other context
BIOSAMPLE
ASSAY
568 results
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ChIP-seq
total RNA-seq
ATAC-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-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
376
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
H1-hESC
8
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