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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
427
ChIP-seq
113
total RNA-seq
ATAC-seq
10
pCHi-C
6
MeRIP-seq
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
2
HiChIP
1
CRISPR RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
CRISPRi RNA-seq
1
GRO-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
427
DNA binding
117
Transcription
4
3D chromatin structure
2
DNA accessibility
1
DNA methylation
1
DNA sequencing
Target of assay
310
transcription factor
89
recombinant protein
78
control
55
RNA binding protein
39
histone
39
histone modification
20
broad histone mark
20
chromatin remodeller
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
87
February, 2021
46
November, 2018
44
August, 2021
30
October, 2019
15
November, 2019
13
March, 2020
6
February, 2023
6
November, 2020
5
January, 2019
5
May, 2021
4
March, 2023
3
December, 2017
1
December, 2018
1
January, 2018
1
May, 2020
1
October, 2022
Available data
515
bam
468
bigWig
371
fastq
342
bed narrowPeak
301
bigBed narrowPeak
122
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
6
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
577
Homo sapiens
Biosample type
tissue
primary cell
573
cell line
in vitro differentiated cells
10
stem cell
Organ
400
liver
73
pancreas
60
blood
bodily fluid
60
epithelium
58
artery
58
blood vessel
58
heart
58
vasculature
19
kidney
8
embryo
1
connective tissue
1
mammary gland
Project
570
AMP
9
T1D
4
community
Genome assembly (visualization)
466
hg19
403
GRCh38
1
hg18
Lab
534
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
4
Anna Gloyn, Oxford
Audit category:
74
inconsistent ontology term
Audit category:
13
missing controlled_by
Audit category:
28
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
biosample_type!
tissue
primary cell
in vitro differentiated cells
assay_title!
ATAC-seq
organ_slims!
bodily fluid
BIOSAMPLE
ASSAY
583 results
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Clear Filters
ChIP-seq
total RNA-seq
pCHi-C
MeRIP-seq
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR RNA-seq
CRISPR genome editing followed by sgRNA sequencing
CRISPRi RNA-seq
GRO-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
14
2
2
2
1
1
EndoC_BH1
15
33
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
Panc1
13
1
1
H1-hESC
8
+ See 13 more…
stem cell
hESC
3
1
SB Ad3.1
1
1
mesenchymal stem cell
1
mesendoderm
1
neural progenitor cell (neural stem cell)
1
+ See 1 more…
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