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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
459
ChIP-seq
48
total RNA-seq
19
ATAC-seq
6
MeRIP-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
Capture-C
2
DNase-seq
2
HiChIP
2
pCHi-C
1
CRISPR genome editing followed by sgRNA sequencing
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
Assay category
459
DNA binding
50
Transcription
21
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
346
transcription factor
89
recombinant protein
77
control
64
RNA binding protein
34
histone
34
histone modification
30
chromatin remodeller
18
broad histone mark
16
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
November, 2018
30
February, 2021
30
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
March, 2020
10
August, 2021
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
511
bam
445
bigWig
427
fastq
377
bed narrowPeak
355
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
49
tsv
14
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
Organism
547
Homo sapiens
Biosample type
2603
tissue
1051
primary cell
551
cell line
386
in vitro differentiated cells
6
stem cell
Organ
370
liver
87
pancreas
74
epithelium
66
artery
66
blood vessel
66
heart
vasculature
61
blood
61
bodily fluid
15
kidney
8
embryo
Project
543
AMP
6
T1D
2
community
Genome assembly (visualization)
444
hg19
395
GRCh38
Lab
538
AMP-T2D consortium
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
84
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
organ_slims!
vasculature
lab.title!
Bing Ren, UCSD
month_released!
March, 2020
BIOSAMPLE
ASSAY
551 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-seq
MeRIP-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
DNase-seq
HiChIP
pCHi-C
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
360
5
1
1
2
1
EndoC_BH1
14
31
17
6
3
1
2
2
1
GM12878
60
1
Panc1
13
1
1
H1-hESC
8
RCC 7860 HIF1a re-expression
4
1
RCC 7860 HIF2a over-expression
3
1
RCC 7860 vector
3
1
EndoC-BH1
1
1
glomerular visceral epithelial cell
1
1
iPSC derived cell line
2
MIN6
1
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