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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
162
ChIP-seq
103
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
2
Capture-C
2
DNase-seq
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
162
DNA binding
105
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
115
transcription factor
30
RNA binding protein
27
control
23
recombinant protein
21
histone
21
histone modification
11
broad histone mark
10
chromatin remodeller
10
narrow histone mark
3
nucleotide modification
Date released
November, 2017
96
February, 2021
56
November, 2018
36
August, 2021
30
October, 2019
28
December, 2018
23
January, 2019
20
May, 2021
16
November, 2019
8
March, 2020
6
November, 2020
2
March, 2023
1
February, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
251
bam
237
bigWig
148
bed narrowPeak
109
tsv
107
fastq
101
bigBed narrowPeak
8
tagAlign
3
bed bed3+
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bed broadPeak
1
bigBed bedMethyl
1
bigBed broadPeak
1
hdf5
1
txt
1
vcf
Organism
321
Homo sapiens
Biosample type
2658
tissue
870
primary cell
351
in vitro differentiated cells
325
cell line
8
stem cell
Organ
88
pancreas
81
liver
75
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
embryo
1
mammary gland
Project
323
AMP
T1D
2
community
Genome assembly (visualization)
247
hg19
230
GRCh38
Lab
283
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
2
Anna Gloyn, Oxford
Audit category:
88
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
1
missing controlled_by
Audit category:
inconsistent control read length
4
inconsistent control run_type
1
inconsistent assembly
audit.WARNING.category!
inconsistent control read length
award.project!
T1D
month_released!
November, 2017
organ_slims!
embryo
BIOSAMPLE
ASSAY
325 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
Capture-C
DNase-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
58
14
1
2
2
2
1
1
EndoC_BH1
13
31
19
6
1
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
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