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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
429
ChIP-seq
77
total RNA-seq
4
STARR-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-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
429
DNA binding
79
Transcription
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
chromatin remodeller
26
histone
26
histone modification
13
broad histone mark
13
narrow histone mark
2
other context
2
other post-translational modification
Date released
300
November, 2017
61
February, 2021
54
November, 2018
41
August, 2021
26
December, 2018
17
January, 2019
15
October, 2019
6
February, 2023
4
March, 2020
2
March, 2023
1
May, 2020
1
October, 2022
Available data
479
bam
431
bigWig
397
fastq
342
bed narrowPeak
323
bigBed narrowPeak
80
tsv
54
bed broadPeak
54
bigBed broadPeak
20
tagAlign
3
tar
2
bed bed3+
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
1
vcf
Organism
524
Homo sapiens
Biosample type
2212
tissue
760
primary cell
528
cell line
243
in vitro differentiated cells
9
stem cell
Organ
380
liver
58
artery
58
blood vessel
58
heart
58
vasculature
50
blood
50
bodily fluid
15
pancreas
8
embryo
3
kidney
2
epithelium
1
mammary gland
Project
521
AMP
5
T1D
2
community
Genome assembly (visualization)
428
hg19
368
GRCh38
Lab
488
AMP-T2D consortium
33
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
inconsistent ontology term
Audit category:
7
missing controlled_by
Audit category:
15
inconsistent control read length
1
inconsistent assembly
assay_slims!
DNA accessibility
audit.ERROR.category!
inconsistent ontology term
month_released!
May, 2023
target.investigated_as!
chromatin remodeller
BIOSAMPLE
ASSAY
528 results
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ChIP-seq
total RNA-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
358
14
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
GM12878
50
Panc1
13
1
H1-hESC
8
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