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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
463
ChIP-seq
28
ATAC-seq
6
MeRIP-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
DNase-seq
2
HiChIP
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
pCHi-C
1
shRNA RNA-seq
1
siRNA RNA-seq
Assay category
463
DNA binding
30
DNA accessibility
3
3D chromatin structure
2
Transcription
1
DNA methylation
Target of assay
347
transcription factor
89
recombinant protein
79
control
63
RNA binding protein
35
histone
35
histone modification
30
chromatin remodeller
18
broad histone mark
17
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
312
November, 2017
61
November, 2018
28
December, 2018
August, 2021
26
October, 2019
18
February, 2021
18
January, 2019
17
May, 2021
15
November, 2019
6
February, 2023
6
November, 2020
2
March, 2020
2
March, 2023
1
January, 2018
1
October, 2022
Available data
574
bam
500
bigWig
427
fastq
390
bed narrowPeak
355
bigBed narrowPeak
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
Organism
509
Homo sapiens
Biosample type
1571
tissue
813
primary cell
513
cell line
228
in vitro differentiated cells
6
stem cell
Organ
361
liver
61
blood
61
bodily fluid
56
pancreas
42
epithelium
14
artery
14
blood vessel
14
heart
14
vasculature
11
kidney
Project
504
AMP
7
T1D
2
community
Genome assembly (visualization)
407
hg19
360
GRCh38
Lab
500
AMP-T2D consortium
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
50
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
tar
month_released!
August, 2021
BIOSAMPLE
ASSAY
513 results
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ChIP-seq
ATAC-seq
MeRIP-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
pCHi-C
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
357
1
1
1
1
GM12878
60
1
EndoC_BH1
15
18
6
3
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
EndoC-BH1
1
1
iPSC derived cell line
2
MIN6
1
glomerular visceral epithelial cell
1
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