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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
29
ATAC-seq
6
MeRIP-seq
5
STARR-seq
5
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
DNase-seq
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
424
DNA binding
115
Transcription
30
DNA accessibility
3
3D chromatin structure
1
DNA sequencing
Target of assay
304
transcription factor
80
control
73
recombinant protein
44
RNA binding protein
38
histone
38
histone modification
23
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
95
February, 2021
November, 2018
44
August, 2021
28
December, 2018
28
October, 2019
23
January, 2019
21
May, 2021
16
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
521
bam
465
bigWig
366
fastq
348
bed narrowPeak
299
bigBed narrowPeak
119
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
hdf5
1
txt
1
vcf
Organism
594
Homo sapiens
Biosample type
2514
tissue
1050
primary cell
598
cell line
364
in vitro differentiated cells
7
stem cell
Organ
354
liver
90
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
46
blood
46
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
587
AMP
9
T1D
2
community
Genome assembly (visualization)
473
hg19
405
GRCh38
Lab
551
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
92
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
10
missing controlled_by
Audit category:
21
inconsistent control read length
4
inconsistent control run_type
files.file_type!
bed bed3+
lab.title!
Struan F.A. Grant, CHOP
month_released!
November, 2018
organ_slims!
nerve
BIOSAMPLE
ASSAY
598 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
DNase-seq
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
333
14
1
2
1
2
1
EndoC_BH1
15
33
19
6
3
1
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
45
1
Panc1
13
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