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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
138
ChIP-seq
19
ATAC-seq
9
total RNA-seq
5
STARR-seq
5
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
3
MeRIP-seq
2
Capture-C
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
shRNA RNA-seq
1
siRNA RNA-seq
Assay category
138
DNA binding
19
DNA accessibility
11
Transcription
3
3D chromatin structure
Target of assay
83
control
52
transcription factor
7
RNA binding protein
6
histone
6
histone modification
3
broad histone mark
3
narrow histone mark
nucleotide modification
2
chromatin remodeller
1
recombinant protein
Date released
98
November, 2017
35
August, 2021
16
May, 2021
10
October, 2019
6
February, 2023
6
March, 2020
4
November, 2018
3
February, 2021
3
January, 2019
3
November, 2019
3
November, 2020
2
March, 2023
1
December, 2018
1
January, 2018
1
May, 2020
1
October, 2022
Available data
119
bam
106
fastq
68
bigWig
46
bed narrowPeak
32
bigBed narrowPeak
15
tsv
14
bed broadPeak
14
bigBed broadPeak
6
tagAlign
3
tar
2
bedpe bed3+
2
hic
bed bed3+
1
txt
vcf
Organism
189
Homo sapiens
Biosample type
915
tissue
545
primary cell
193
cell line
123
in vitro differentiated cells
7
stem cell
Organ
131
liver
34
pancreas
27
epithelium
7
blood
7
bodily fluid
7
kidney
2
artery
2
blood vessel
2
heart
2
vasculature
1
mammary gland
Project
186
AMP
5
T1D
2
community
Genome assembly (visualization)
527
hg19
GRCh38
Lab
150
AMP-T2D consortium
33
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
3
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
Audit category:
32
inconsistent ontology term
Audit category:
8
missing controlled_by
Audit category:
4
inconsistent control read length
2
inconsistent control run_type
assembly!
GRCh38
files.file_type!
bed bed3+
vcf
target.investigated_as!
nucleotide modification
BIOSAMPLE
ASSAY
193 results
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ChIP-seq
ATAC-seq
total RNA-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
MeRIP-seq
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
117
9
2
1
2
EndoC_BH1
2
18
3
1
3
2
2
1
GM12878
6
1
Panc1
7
EndoC-BH1
1
1
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