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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
435
ChIP-seq
113
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
5
STARR-seq
5
pCHi-C
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
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
435
DNA binding
115
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
89
recombinant protein
83
control
65
RNA binding protein
38
histone
38
histone modification
chromatin remodeller
19
broad histone mark
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
293
November, 2017
96
February, 2021
54
November, 2018
42
August, 2021
27
October, 2019
26
December, 2018
20
May, 2021
16
January, 2019
12
November, 2019
10
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
May, 2020
1
October, 2022
Available data
535
bam
473
bigWig
389
fastq
356
bed narrowPeak
315
bigBed narrowPeak
118
tsv
49
bed broadPeak
49
bigBed broadPeak
15
tagAlign
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
608
Homo sapiens
Biosample type
2279
tissue
823
primary cell
612
cell line
336
in vitro differentiated cells
9
stem cell
Organ
371
liver
83
pancreas
73
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
50
blood
50
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
603
AMP
7
T1D
2
community
Genome assembly (visualization)
481
hg19
420
GRCh38
Lab
567
AMP-T2D consortium
32
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
86
inconsistent ontology term
1
inconsistent replicate
Audit category:
6
missing controlled_by
Audit category:
10
inconsistent control read length
1
inconsistent assembly
files.file_type!
csv
month_released!
May, 2020
target.investigated_as!
chromatin remodeller
narrow histone mark
BIOSAMPLE
ASSAY
612 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
STARR-seq
pCHi-C
Hi-C
CRISPR genome editing followed by DNA sequencing
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
349
14
1
2
1
2
1
1
EndoC_BH1
9
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
49
1
Panc1
10
1
1
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