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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
465
ChIP-seq
100
total RNA-seq
13
ATAC-seq
6
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
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
Assay category
465
DNA binding
102
Transcription
15
DNA accessibility
3
3D chromatin structure
1
DNA methylation
Target of assay
350
transcription factor
89
recombinant protein
76
control
64
RNA binding protein
34
histone
34
histone modification
30
chromatin remodeller
18
broad histone mark
16
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
96
February, 2021
61
November, 2018
30
October, 2019
28
December, 2018
23
January, 2019
May, 2021
16
November, 2019
11
March, 2020
10
August, 2021
6
February, 2023
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
577
bam
503
bigWig
427
fastq
389
bed narrowPeak
355
bigBed narrowPeak
106
tsv
59
bed broadPeak
59
bigBed broadPeak
20
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
597
Homo sapiens
Biosample type
2729
tissue
882
primary cell
601
cell line
262
in vitro differentiated cells
10
stem cell
Organ
370
liver
66
artery
66
blood vessel
66
heart
66
vasculature
65
pancreas
61
blood
61
bodily fluid
52
epithelium
17
kidney
8
embryo
1
mammary gland
Project
591
AMP
8
T1D
2
community
Genome assembly (visualization)
510
hg19
459
GRCh38
Lab
594
AMP-T2D consortium
Bing Ren, UCSD
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
64
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
month_released!
May, 2021
lab.title!
Rohit N. Kulkarni, M.D., Ph.D.
Bing Ren, UCSD
BIOSAMPLE
ASSAY
601 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
360
5
1
2
1
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
EndoC_BH1
14
29
3
3
1
2
2
1
Panc1
13
1
1
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