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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
448
ChIP-seq
total RNA-seq
21
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
DNase-seq
2
HiChIP
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
448
DNA binding
23
DNA accessibility
4
3D chromatin structure
2
Transcription
1
DNA methylation
1
DNA sequencing
Target of assay
357
transcription factor
89
recombinant protein
81
control
65
RNA binding protein
38
histone
38
histone modification
chromatin remodeller
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
300
November, 2017
54
November, 2018
27
August, 2021
26
December, 2018
26
October, 2019
17
May, 2021
15
November, 2019
12
January, 2019
7
March, 2020
6
February, 2023
6
November, 2020
4
February, 2021
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
434
bam
392
fastq
384
bigWig
362
bed narrowPeak
325
bigBed narrowPeak
55
bed broadPeak
55
bigBed broadPeak
14
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
501
Homo sapiens
Biosample type
1440
tissue
831
primary cell
505
cell line
255
in vitro differentiated cells
10
stem cell
Organ
367
liver
59
pancreas
51
blood
51
bodily fluid
45
epithelium
15
kidney
14
artery
14
blood vessel
heart
14
vasculature
1
mammary gland
Project
496
AMP
7
T1D
2
community
Genome assembly (visualization)
384
hg19
320
GRCh38
Lab
467
AMP-T2D consortium
25
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
56
inconsistent ontology term
1
inconsistent replicate
Audit category:
7
missing controlled_by
Audit category:
15
inconsistent control read length
1
inconsistent assembly
organ_slims!
heart
assay_title!
total RNA-seq
target.investigated_as!
chromatin remodeller
BIOSAMPLE
ASSAY
505 results
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ChIP-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
358
1
2
2
2
1
1
GM12878
50
1
EndoC_BH1
15
19
6
1
3
2
2
1
Panc1
13
1
1
RCC 7860 HIF1a re-expression
4
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