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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
457
ChIP-seq
35
total RNA-seq
20
ATAC-seq
6
MeRIP-seq
5
STARR-seq
5
pCHi-C
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
457
DNA binding
37
Transcription
22
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
356
transcription factor
89
recombinant protein
80
control
65
RNA binding protein
38
histone
38
histone modification
30
chromatin remodeller
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
307
November, 2017
February, 2021
61
November, 2018
43
August, 2021
28
December, 2018
26
October, 2019
23
January, 2019
21
May, 2021
11
March, 2020
10
November, 2019
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
469
bam
421
bigWig
419
fastq
373
bed narrowPeak
345
bigBed narrowPeak
51
bed broadPeak
51
bigBed broadPeak
41
tsv
6
tagAlign
3
tar
2
bed bed3+
2
bedpe bed3+
2
hic
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
543
Homo sapiens
Biosample type
1909
tissue
918
primary cell
547
cell line
312
in vitro differentiated cells
9
stem cell
Organ
390
liver
61
blood
61
bodily fluid
56
pancreas
47
epithelium
19
kidney
8
embryo
1
mammary gland
Project
536
AMP
9
T1D
2
community
Genome assembly (visualization)
419
hg19
356
GRCh38
Lab
501
AMP-T2D consortium
33
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
60
inconsistent ontology term
1
inconsistent control
Audit category:
13
missing controlled_by
Audit category:
20
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
target.investigated_as!
broad histone mark
month_released!
February, 2021
BIOSAMPLE
ASSAY
547 results
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ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
STARR-seq
pCHi-C
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
369
14
2
1
2
1
1
GM12878
60
1
EndoC_BH1
9
7
19
6
1
3
2
2
1
Panc1
9
1
1
H1-hESC
8
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