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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
478
ChIP-seq
61
total RNA-seq
20
ATAC-seq
6
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 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
478
DNA binding
63
Transcription
22
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
357
transcription factor
89
recombinant protein
81
control
65
RNA binding protein
38
histone
38
histone modification
30
chromatin remodeller
19
broad histone mark
19
narrow histone mark
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
November, 2018
44
August, 2021
30
October, 2019
29
February, 2021
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
11
March, 2020
6
February, 2023
3
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
516
bam
466
bigWig
427
fastq
392
bed narrowPeak
355
bigBed narrowPeak
67
tsv
59
bed broadPeak
59
bigBed broadPeak
14
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
588
Homo sapiens
Biosample type
2457
tissue
1074
primary cell
592
cell line
388
in vitro differentiated cells
10
stem cell
Organ
400
liver
89
pancreas
76
epithelium
66
artery
66
blood vessel
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
581
AMP
9
T1D
2
community
Genome assembly (visualization)
465
hg19
399
GRCh38
Lab
548
AMP-T2D consortium
34
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
3
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
Audit category:
89
inconsistent ontology term
1
inconsistent control
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
files.file_type!
bed bed3
organ_slims!
heart
target.investigated_as!
nucleotide modification
BIOSAMPLE
ASSAY
592 results
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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 genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
14
2
2
2
1
1
EndoC_BH1
15
33
19
1
3
3
2
2
1
GM12878
60
1
Panc1
13
1
1
H1-hESC
8
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