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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
451
ChIP-seq
70
total RNA-seq
10
ATAC-seq
6
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
2
Hi-C
2
HiChIP
1
DNase-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
Assay category
451
DNA binding
72
Transcription
11
DNA accessibility
2
3D chromatin structure
1
DNA methylation
Target of assay
349
transcription factor
89
recombinant protein
74
control
63
RNA binding protein
30
chromatin remodeller
23
histone
23
histone modification
12
broad histone mark
11
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
70
February, 2021
61
November, 2018
28
December, 2018
28
October, 2019
23
January, 2019
8
August, 2021
6
March, 2020
5
February, 2023
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
531
bam
458
bigWig
427
fastq
375
bed narrowPeak
354
bigBed narrowPeak
75
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
Organism
546
Homo sapiens
Biosample type
2718
tissue
682
primary cell
549
cell line
370
in vitro differentiated cells
10
stem cell
Organ
370
liver
92
pancreas
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
17
kidney
8
embryo
1
mammary gland
Project
542
AMP
5
T1D
2
community
Genome assembly (visualization)
463
hg19
415
GRCh38
Lab
542
AMP-T2D consortium
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
15
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!
epithelium
lab.title!
Bing Ren, UCSD
BIOSAMPLE
ASSAY
549 results
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ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
HiChIP
DNase-seq
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
Panc1
13
1
1
H1-hESC
8
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