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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
129
ChIP-seq
9
total RNA-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
2
Hi-C
2
HiChIP
1
ATAC-seq
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
1
whole genome sequencing assay
Assay category
129
DNA binding
11
Transcription
2
3D chromatin structure
1
DNA accessibility
1
DNA sequencing
Target of assay
72
control
52
transcription factor
7
RNA binding protein
5
histone
5
histone modification
3
narrow histone mark
2
broad histone mark
2
chromatin remodeller
1
recombinant protein
Date released
98
November, 2017
34
August, 2021
5
February, 2023
4
February, 2021
4
March, 2020
4
November, 2018
3
January, 2019
3
October, 2019
2
March, 2023
1
December, 2018
1
January, 2018
1
May, 2020
1
October, 2022
Available data
110
bam
106
fastq
66
bigWig
46
bed narrowPeak
32
bigBed narrowPeak
14
bed broadPeak
14
bigBed broadPeak
14
tsv
6
tagAlign
3
tar
1
bed bed3+
1
bedpe bed3+
1
hic
1
txt
1
vcf
Organism
158
Homo sapiens
Biosample type
799
tissue
398
primary cell
161
cell line
128
in vitro differentiated cells
7
stem cell
Organ
133
liver
pancreas
30
epithelium
7
blood
7
bodily fluid
7
kidney
2
artery
2
blood vessel
2
heart
2
vasculature
1
mammary gland
Project
154
AMP
5
T1D
2
community
Genome assembly (visualization)
472
hg19
GRCh38
Lab
120
AMP-T2D consortium
34
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
6
inconsistent ontology term
Audit category:
8
missing controlled_by
Audit category:
4
inconsistent control read length
2
inconsistent control run_type
assembly!
GRCh38
organ_slims!
pancreas
BIOSAMPLE
ASSAY
161 results
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Clear Filters
ChIP-seq
total RNA-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
HiChIP
ATAC-seq
MPRA
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
117
9
2
2
2
1
GM12878
6
1
EndoC_BH1
3
2
EndoC-BH1
1
1
HEK293T
2
RCC 7860 vector
1
1
smooth muscle cell of the coronary artery
2
MCF-7
1
MIN6
1
RCC 7860 HIF1a re-expression
1
RCC 7860 HIF2a over-expression
1
RCC 7860 VHL
1
Synthesized DNA
1
fibroblast cell line
1
iPSC derived cell line
1
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