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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
125
ChIP-seq
61
total RNA-seq
21
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
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
125
DNA binding
63
Transcription
21
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
81
control
29
transcription factor
18
histone
18
histone modification
9
broad histone mark
9
narrow histone mark
8
recombinant protein
4
RNA binding protein
3
nucleotide modification
Date released
66
November, 2017
44
August, 2021
30
February, 2021
22
October, 2019
21
May, 2021
16
November, 2019
11
March, 2020
8
January, 2019
6
February, 2023
6
November, 2020
5
November, 2018
2
March, 2023
1
December, 2018
1
January, 2018
1
May, 2020
1
October, 2022
Available data
516
bam
466
bigWig
427
fastq
392
bed narrowPeak
bigBed narrowPeak
67
tsv
59
bed broadPeak
59
bigBed broadPeak
14
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
237
Homo sapiens
Biosample type
1987
tissue
963
primary cell
377
in vitro differentiated cells
241
cell line
10
stem cell
Organ
108
liver
85
pancreas
78
epithelium
66
artery
66
blood vessel
66
heart
vasculature
18
kidney
8
embryo
7
blood
7
bodily fluid
1
mammary gland
Project
230
AMP
9
T1D
2
community
Genome assembly (visualization)
115
hg19
77
GRCh38
Lab
194
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:
92
inconsistent ontology term
1
inconsistent replicate
Audit category:
1
missing controlled_by
Audit category:
2
inconsistent control read length
1
inconsistent assembly
files.file_type!
bigBed narrowPeak
lab.title!
Katalin Susztak, Upenn
month_released!
April, 2019
organ_slims!
vasculature
BIOSAMPLE
ASSAY
241 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
85
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
H1-hESC
8
Panc1
7
1
GM12878
6
1
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