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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
467
ChIP-seq
113
total RNA-seq
29
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
467
DNA binding
117
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
356
transcription factor
89
recombinant protein
80
control
65
RNA binding protein
30
chromatin remodeller
29
histone
29
histone modification
15
narrow histone mark
14
broad histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
303
November, 2017
88
February, 2021
61
November, 2018
44
August, 2021
30
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
15
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
585
bam
525
bigWig
431
fastq
406
bed narrowPeak
355
bigBed narrowPeak
123
tsv
59
bed broadPeak
59
bigBed broadPeak
tagAlign
6
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
646
Homo sapiens
Biosample type
2539
tissue
988
primary cell
642
cell line
354
in vitro differentiated cells
10
stem cell
Organ
389
liver
92
pancreas
79
epithelium
61
blood
61
bodily fluid
60
artery
60
blood vessel
60
heart
60
vasculature
19
kidney
8
embryo
1
connective tissue
1
mammary gland
Project
639
AMP
9
T1D
4
community
Genome assembly (visualization)
516
hg19
453
GRCh38
1
hg18
Lab
603
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:
93
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
17
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
files.file_type!
tagAlign
BIOSAMPLE
ASSAY
652 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-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
366
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
GM12878
60
1
smooth muscle cell of the coronary artery
52
8
Panc1
13
1
1
+ 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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