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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
474
ChIP-seq
111
total RNA-seq
29
ATAC-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
474
DNA binding
111
Transcription
31
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
353
transcription factor
89
recombinant protein
80
control
62
RNA binding protein
36
histone
36
histone modification
22
chromatin remodeller
19
broad histone mark
17
narrow histone mark
2
other context
2
other post-translational modification
Date released
311
November, 2017
96
February, 2021
57
November, 2018
44
August, 2021
30
October, 2019
28
December, 2018
23
January, 2019
20
May, 2021
16
November, 2019
8
March, 2020
1
February, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
570
bam
510
bigWig
419
fastq
394
bed narrowPeak
347
bigBed narrowPeak
117
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
635
Homo sapiens
Biosample type
2676
tissue
637
cell line
558
primary cell
394
in vitro differentiated cells
8
stem cell
Organ
393
liver
82
pancreas
69
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
637
AMP
9
T1D
2
community
Genome assembly (visualization)
518
hg19
454
GRCh38
Lab
603
AMP-T2D consortium
34
Bing Ren, UCSD
Rohit N. Kulkarni, M.D., Ph.D.
Audit category:
82
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
7
missing controlled_by
Audit category:
26
inconsistent control read length
inconsistent control run_type
1
inconsistent assembly
assay_title!
CRISPRi RNA-seq
audit.WARNING.category!
inconsistent control run_type
lab.title!
Rohit N. Kulkarni, M.D., Ph.D.
BIOSAMPLE
ASSAY
637 results
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ChIP-seq
total RNA-seq
ATAC-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
370
14
1
2
2
2
1
1
EndoC_BH1
13
31
19
1
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
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