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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
424
ChIP-seq
113
total RNA-seq
6
MeRIP-seq
6
pCHi-C
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
424
DNA binding
115
Transcription
DNA accessibility
4
3D chromatin structure
1
DNA sequencing
Target of assay
310
transcription factor
89
recombinant protein
77
control
55
RNA binding protein
37
histone
37
histone modification
20
chromatin remodeller
19
broad histone mark
18
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
87
February, 2021
45
November, 2018
39
August, 2021
28
October, 2019
15
November, 2019
9
March, 2020
6
February, 2023
6
November, 2020
5
January, 2019
5
May, 2021
2
March, 2023
1
December, 2018
1
May, 2020
1
October, 2022
Available data
510
bam
463
bigWig
367
fastq
338
bed narrowPeak
299
bigBed narrowPeak
118
tsv
58
bed broadPeak
58
bigBed broadPeak
20
tagAlign
3
tar
2
bed bed3+
2
bedpe bed3+
2
hic
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
561
Homo sapiens
Biosample type
2282
tissue
790
primary cell
565
cell line
351
in vitro differentiated cells
10
stem cell
Organ
397
liver
72
pancreas
60
blood
bodily fluid
59
epithelium
58
artery
58
blood vessel
58
heart
58
vasculature
16
kidney
8
embryo
1
mammary gland
Project
554
AMP
9
T1D
2
community
Genome assembly (visualization)
461
hg19
397
GRCh38
Lab
523
AMP-T2D consortium
29
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
72
inconsistent ontology term
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_slims!
DNA accessibility
assay_title!
STARR-seq
files.file_type!
bed bedMethyl
organ_slims!
bodily fluid
BIOSAMPLE
ASSAY
565 results
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Clear Filters
ChIP-seq
total RNA-seq
MeRIP-seq
pCHi-C
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
14
2
2
1
EndoC_BH1
15
33
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
Panc1
13
1
H1-hESC
8
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