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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
482
ChIP-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
whole genome sequencing assay
Assay category
482
DNA binding
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
89
recombinant protein
83
control
65
RNA binding protein
36
histone
36
histone modification
30
chromatin remodeller
19
broad histone mark
17
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
November, 2018
28
December, 2018
27
August, 2021
26
October, 2019
18
February, 2021
18
January, 2019
16
May, 2021
15
November, 2019
6
March, 2020
6
November, 2020
1
February, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
476
bam
422
fastq
416
bigWig
402
bed narrowPeak
355
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
6
tsv
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
538
Homo sapiens
Biosample type
1486
tissue
544
primary cell
540
cell line
256
in vitro differentiated cells
8
stem cell
Organ
387
liver
61
blood
61
bodily fluid
57
pancreas
43
epithelium
15
kidney
14
artery
14
blood vessel
14
heart
14
vasculature
1
mammary gland
Project
540
AMP
T1D
Genome assembly (visualization)
424
hg19
358
GRCh38
Lab
509
AMP-T2D consortium
25
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
Audit category:
54
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_slims!
Transcription
award.project!
T1D
BIOSAMPLE
ASSAY
540 results
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ChIP-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
Capture-C
DNase-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
whole genome sequencing assay
cell line
HepG2
378
1
2
2
2
1
1
GM12878
60
1
EndoC_BH1
13
19
6
1
2
1
Panc1
13
1
1
smooth muscle cell of the coronary artery
6
8
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