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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
446
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
446
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
broad histone mark
13
narrow histone mark
2
other context
2
other post-translational modification
Date released
307
November, 2017
70
February, 2021
61
November, 2018
40
August, 2021
28
December, 2018
23
January, 2019
13
October, 2019
6
February, 2023
4
March, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
508
bam
452
bigWig
419
fastq
372
bed narrowPeak
345
bigBed narrowPeak
80
tsv
51
bed broadPeak
51
bigBed broadPeak
14
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
553
Homo sapiens
Biosample type
2221
tissue
890
primary cell
557
cell line
223
in vitro differentiated cells
8
stem cell
Organ
392
liver
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
12
pancreas
8
embryo
4
kidney
3
epithelium
1
mammary gland
Project
550
AMP
5
T1D
2
community
Genome assembly (visualization)
458
hg19
397
GRCh38
Lab
518
AMP-T2D consortium
32
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:
20
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
audit.ERROR.category!
inconsistent ontology term
month_released!
June, 2019
target.investigated_as!
broad histone mark
BIOSAMPLE
ASSAY
557 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
369
14
1
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
9
1
1
H1-hESC
8
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