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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
472
ChIP-seq
79
total RNA-seq
10
ATAC-seq
10
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
HiChIP
1
CRISPR RNA-seq
1
CRISPRi RNA-seq
1
DNase-seq
1
GRO-seq
1
MPRA
1
WGBS
1
shRNA RNA-seq
1
siRNA RNA-seq
Assay category
472
DNA binding
83
Transcription
11
DNA accessibility
3
3D chromatin structure
1
DNA methylation
DNA sequencing
Target of assay
360
transcription factor
89
recombinant protein
79
control
64
RNA binding protein
30
chromatin remodeller
28
histone
28
histone modification
14
broad histone mark
14
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
70
February, 2021
61
November, 2018
41
August, 2021
28
December, 2018
28
October, 2019
23
January, 2019
10
March, 2020
5
February, 2023
4
March, 2023
3
December, 2017
2
January, 2018
1
May, 2020
1
October, 2022
Available data
534
bam
475
bigWig
431
fastq
391
bed narrowPeak
354
bigBed narrowPeak
88
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
6
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
Organism
587
Homo sapiens
Biosample type
2747
tissue
682
primary cell
582
cell line
370
in vitro differentiated cells
10
stem cell
Organ
400
liver
92
pancreas
epithelium
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
8
embryo
1
connective tissue
1
mammary gland
Project
583
AMP
5
T1D
4
community
Genome assembly (visualization)
481
hg19
418
GRCh38
1
hg18
Lab
550
AMP-T2D consortium
33
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
4
Anna Gloyn, Oxford
Audit category:
17
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
28
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_slims!
DNA sequencing
month_released!
May, 2023
organ_slims!
epithelium
BIOSAMPLE
ASSAY
592 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
HiChIP
CRISPR RNA-seq
CRISPRi RNA-seq
DNase-seq
GRO-seq
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
378
14
1
2
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
H1-hESC
8
+ See 13 more…
stem cell
hESC
3
1
SB Ad3.1
1
1
mesenchymal stem cell
1
mesendoderm
1
neural progenitor cell (neural stem cell)
1
+ See 1 more…
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