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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
399
ChIP-seq
77
total RNA-seq
9
ATAC-seq
4
STARR-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
2
DNase-seq
2
Hi-C
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
399
DNA binding
79
Transcription
11
DNA accessibility
2
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
302
transcription factor
82
recombinant protein
69
control
54
RNA binding protein
25
histone
25
histone modification
20
chromatin remodeller
13
broad histone mark
12
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
70
February, 2021
46
November, 2018
41
August, 2021
16
October, 2019
6
February, 2023
5
January, 2019
4
March, 2020
2
March, 2023
1
December, 2018
1
May, 2020
1
October, 2022
Available data
460
bam
409
bigWig
367
fastq
329
bed narrowPeak
301
bigBed narrowPeak
80
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
hdf5
1
hic
1
txt
1
vcf
Organism
504
Homo sapiens
Biosample type
2686
tissue
1022
primary cell
508
cell line
279
in vitro differentiated cells
9
stem cell
Organ
401
liver
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
bodily fluid
15
pancreas
8
embryo
4
kidney
3
epithelium
1
mammary gland
Project
501
AMP
5
T1D
2
community
Genome assembly (visualization)
414
hg19
352
GRCh38
Lab
468
AMP-T2D consortium
33
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
inconsistent ontology term
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
organ_slims!
bodily fluid
files.file_type!
hdf5
audit.ERROR.category!
inconsistent ontology term
BIOSAMPLE
ASSAY
508 results
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ChIP-seq
total RNA-seq
ATAC-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
DNase-seq
Hi-C
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
1
2
2
2
1
1
smooth muscle cell of the coronary artery
6
52
8
Panc1
13
1
H1-hESC
8
EndoC_BH1
3
2
1
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