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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
446
ChIP-seq
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
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
446
DNA binding
31
DNA accessibility
4
3D chromatin structure
2
Transcription
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
89
recombinant protein
83
control
65
RNA binding protein
histone
38
histone modification
30
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
300
November, 2017
61
November, 2018
28
December, 2018
24
August, 2021
19
October, 2019
18
February, 2021
17
January, 2019
16
May, 2021
6
February, 2023
6
March, 2020
6
November, 2020
5
November, 2019
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
443
bam
406
fastq
381
bigWig
369
bed narrowPeak
335
bigBed narrowPeak
45
bed broadPeak
45
bigBed broadPeak
9
tagAlign
6
tsv
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
507
Homo sapiens
Biosample type
1052
tissue
604
primary cell
511
cell line
146
in vitro differentiated cells
8
stem cell
Organ
369
liver
60
blood
60
bodily fluid
40
pancreas
33
epithelium
15
kidney
14
artery
14
blood vessel
14
heart
14
vasculature
1
mammary gland
Project
504
AMP
5
T1D
2
community
Genome assembly (visualization)
389
hg19
328
GRCh38
Lab
476
AMP-T2D consortium
22
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
44
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
12
missing controlled_by
Audit category:
15
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_title!
total RNA-seq
month_released!
April, 2019
September, 2023
target.investigated_as!
histone
BIOSAMPLE
ASSAY
511 results
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ChIP-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
360
1
2
2
2
1
1
GM12878
59
1
EndoC_BH1
3
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
8
Panc1
6
1
1
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