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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
482
ChIP-seq
28
ATAC-seq
6
MeRIP-seq
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
pCHi-C
1
whole genome sequencing assay
Assay category
482
DNA binding
30
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
November, 2020
1
February, 2023
1
January, 2018
1
March, 2020
1
October, 2022
Available data
578
bam
518
bigWig
427
fastq
402
bed narrowPeak
355
bigBed narrowPeak
tsv
59
bed broadPeak
59
bigBed broadPeak
20
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
532
Homo sapiens
Biosample type
1564
tissue
534
cell line
391
primary cell
263
in vitro differentiated cells
4
stem cell
Organ
386
liver
61
blood
61
bodily fluid
56
pancreas
42
epithelium
14
artery
14
blood vessel
14
heart
14
vasculature
13
kidney
Project
534
AMP
7
T1D
2
community
Genome assembly (visualization)
423
hg19
358
GRCh38
Lab
503
AMP-T2D consortium
25
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
Audit category:
51
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
files.file_type!
tsv
BIOSAMPLE
ASSAY
534 results
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ChIP-seq
ATAC-seq
MeRIP-seq
STARR-seq
Hi-C
Capture-C
DNase-seq
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
pCHi-C
whole genome sequencing assay
cell line
HepG2
378
1
2
2
1
1
1
GM12878
60
1
EndoC_BH1
13
18
6
1
2
1
Panc1
13
1
1
smooth muscle cell of the coronary artery
6
8
RCC 7860 HIF1a re-expression
4
RCC 7860 HIF2a over-expression
3
RCC 7860 vector
3
HEK293T
2
iPSC derived cell line
2
MIN6
1
Synthesized DNA
1
glomerular visceral epithelial cell
1
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