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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
441
ChIP-seq
72
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
441
DNA binding
74
Transcription
12
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
339
transcription factor
82
recombinant protein
72
control
58
RNA binding protein
25
histone
25
histone modification
24
chromatin remodeller
13
broad histone mark
12
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
70
February, 2021
61
November, 2018
41
August, 2021
28
December, 2018
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
497
bam
444
bigWig
404
fastq
368
bed narrowPeak
340
bigBed narrowPeak
75
tsv
59
bed broadPeak
59
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
543
Homo sapiens
Biosample type
2678
tissue
1034
primary cell
547
cell line
279
in vitro differentiated cells
9
stem cell
Organ
396
liver
66
artery
66
blood vessel
66
heart
66
vasculature
43
blood
43
bodily fluid
16
pancreas
8
embryo
4
kidney
3
epithelium
1
mammary gland
Project
540
AMP
5
T1D
2
community
Genome assembly (visualization)
450
hg19
387
GRCh38
Lab
507
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
month_released!
January, 2019
organ_slims!
adrenal gland
BIOSAMPLE
ASSAY
547 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
378
9
1
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
42
1
Panc1
13
1
1
H1-hESC
8
EndoC_BH1
3
2
1
EndoC-BH1
1
1
HEK293T
2
early embryonic cell
2
glomerular visceral epithelial cell
1
1
iPSC derived cell line
2
MCF-7
1
MIN6
1
fibroblast cell line
1
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