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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
19
ATAC-seq
19
ChIP-seq
9
total RNA-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
Hi-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
19
DNA accessibility
19
DNA binding
11
Transcription
2
3D chromatin structure
1
DNA sequencing
Target of assay
12
transcription factor
7
control
3
histone
3
histone modification
3
nucleotide modification
2
narrow histone mark
1
RNA binding protein
1
broad histone mark
Date released
35
August, 2021
16
May, 2021
6
February, 2023
6
March, 2020
6
November, 2020
2
March, 2023
1
December, 2018
1
February, 2021
1
January, 2018
1
May, 2020
1
November, 2017
1
October, 2019
1
October, 2022
Available data
bam
522
bigWig
427
fastq
404
bed narrowPeak
355
bigBed narrowPeak
119
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
74
Homo sapiens
Biosample type
820
tissue
475
primary cell
96
in vitro differentiated cells
78
cell line
7
stem cell
Organ
34
liver
28
pancreas
27
epithelium
4
kidney
1
blood
1
bodily fluid
1
mammary gland
Project
71
AMP
5
T1D
2
community
Genome assembly (visualization)
19
hg19
1
GRCh38
Lab
33
Bing Ren, UCSD
32
AMP-T2D consortium
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
29
inconsistent ontology term
Audit category:
1
inconsistent assembly
files.file_type!
bedpe bed3+
bam
BIOSAMPLE
ASSAY
78 results
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Clear Filters
ATAC-seq
ChIP-seq
total RNA-seq
MeRIP-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Capture-C
Hi-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
19
9
2
2
1
1
EndoC_BH1
18
6
3
2
2
1
EndoC-BH1
1
1
HEK293T
2
GM12878
1
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