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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
450
ChIP-seq
109
total RNA-seq
29
ATAC-seq
8
pCHi-C
6
MeRIP-seq
3
CRISPR genome editing followed by DNA sequencing
3
STARR-seq
2
Capture-C
2
Hi-C
2
HiChIP
1
CRISPR RNA-seq
1
CRISPR genome editing followed by sgRNA sequencing
1
CRISPRi RNA-seq
1
DNase-seq
1
GRO-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
450
DNA binding
113
Transcription
30
DNA accessibility
2
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
329
transcription factor
82
recombinant protein
81
control
63
RNA binding protein
40
histone
40
histone modification
28
chromatin remodeller
20
broad histone mark
20
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
96
February, 2021
61
November, 2018
42
August, 2021
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
14
October, 2019
13
March, 2020
6
February, 2023
6
November, 2020
4
March, 2023
3
December, 2017
2
January, 2018
1
May, 2020
1
October, 2022
Available data
543
bam
485
bigWig
403
fastq
371
bed narrowPeak
327
bigBed narrowPeak
117
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
5
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
txt
1
vcf
Organism
618
Homo sapiens
Biosample type
2470
tissue
1050
primary cell
614
cell line
394
in vitro differentiated cells
10
stem cell
Organ
400
liver
91
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
34
blood
34
bodily fluid
kidney
8
embryo
1
connective tissue
1
mammary gland
Project
611
AMP
9
T1D
4
community
Genome assembly (visualization)
493
hg19
427
GRCh38
1
hg18
Lab
577
AMP-T2D consortium
32
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
4
Anna Gloyn, Oxford
Audit category:
78
inconsistent ontology term
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
28
inconsistent control read length
8
inconsistent control run_type
inconsistent assembly
audit.WARNING.category!
inconsistent assembly
month_released!
December, 2018
organ_slims!
kidney
BIOSAMPLE
ASSAY
624 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
MeRIP-seq
CRISPR genome editing followed by DNA sequencing
STARR-seq
Capture-C
Hi-C
HiChIP
CRISPR RNA-seq
CRISPR genome editing followed by sgRNA sequencing
CRISPRi RNA-seq
DNase-seq
GRO-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
14
1
2
2
1
1
1
EndoC_BH1
15
33
19
6
3
2
1
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
33
1
Panc1
13
1
+ See 8 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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