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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
365
ChIP-seq
113
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
365
DNA binding
115
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
recombinant protein
83
control
65
RNA binding protein
38
histone
38
histone modification
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
234
November, 2017
96
February, 2021
44
August, 2021
38
November, 2018
26
December, 2018
23
October, 2019
21
May, 2021
17
January, 2019
16
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
463
bam
404
bigWig
315
fastq
286
bed narrowPeak
244
bigBed narrowPeak
119
tsv
55
bed broadPeak
55
bigBed broadPeak
20
tagAlign
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
539
Homo sapiens
Biosample type
2775
tissue
1087
primary cell
543
cell line
391
in vitro differentiated cells
9
stem cell
Organ
299
liver
92
pancreas
79
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
51
blood
51
bodily fluid
12
kidney
8
embryo
1
mammary gland
Project
532
AMP
9
T1D
2
community
Genome assembly (visualization)
415
hg19
348
GRCh38
Lab
496
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
85
inconsistent ontology term
1
inconsistent replicate
Audit category:
6
missing controlled_by
Audit category:
14
inconsistent control read length
1
inconsistent assembly
target.investigated_as!
recombinant protein
chromatin remodeller
assay_title!
CRISPRi RNA-seq
BIOSAMPLE
ASSAY
543 results
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ChIP-seq
total RNA-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
276
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
50
1
Panc1
13
1
1
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