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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
449
ChIP-seq
79
total RNA-seq
10
ATAC-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
HiChIP
1
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
449
DNA binding
81
Transcription
11
DNA accessibility
3
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
355
transcription factor
89
recombinant protein
74
control
64
RNA binding protein
30
chromatin remodeller
15
histone
15
histone modification
8
narrow histone mark
7
broad histone mark
2
other context
2
other post-translational modification
Date released
303
November, 2017
62
February, 2021
61
November, 2018
42
August, 2021
28
December, 2018
28
October, 2019
23
January, 2019
6
March, 2020
5
February, 2023
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
531
bam
472
bigWig
427
fastq
389
bed narrowPeak
354
bigBed narrowPeak
84
tsv
59
bed broadPeak
59
bigBed broadPeak
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
560
Homo sapiens
Biosample type
2484
tissue
586
primary cell
563
cell line
333
in vitro differentiated cells
10
stem cell
Organ
389
liver
92
pancreas
epithelium
61
blood
61
bodily fluid
60
artery
60
blood vessel
60
heart
60
vasculature
19
kidney
8
embryo
1
mammary gland
Project
556
AMP
5
T1D
2
community
Genome assembly (visualization)
461
hg19
401
GRCh38
Lab
522
AMP-T2D consortium
34
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
16
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
15
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
organ_slims!
epithelium
files.file_type!
tagAlign
BIOSAMPLE
ASSAY
563 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
HiChIP
DNase-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
366
14
1
2
2
2
1
1
GM12878
60
1
smooth muscle cell of the coronary artery
52
8
Panc1
13
1
1
H1-hESC
8
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