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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
471
ChIP-seq
total RNA-seq
29
ATAC-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
3
CRISPR genome editing followed by DNA sequencing
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
1
whole genome sequencing assay
Assay category
471
DNA binding
31
DNA accessibility
4
3D chromatin structure
2
Transcription
1
DNA methylation
1
DNA sequencing
Target of assay
349
transcription factor
88
recombinant protein
83
control
63
RNA binding protein
37
histone
37
histone modification
24
chromatin remodeller
19
broad histone mark
18
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
305
November, 2017
58
November, 2018
28
December, 2018
27
August, 2021
26
October, 2019
18
February, 2021
18
January, 2019
17
May, 2021
15
November, 2019
7
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
465
bam
409
fastq
406
bigWig
392
bed narrowPeak
343
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
6
tsv
3
bed bed3+
3
tar
2
bedpe bed3+
2
hic
1
bed bed3
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
txt
1
vcf
Organism
532
Homo sapiens
Biosample type
1674
tissue
797
primary cell
536
cell line
252
in vitro differentiated cells
10
stem cell
Organ
374
liver
61
blood
61
bodily fluid
59
pancreas
45
epithelium
15
kidney
14
artery
14
blood vessel
14
heart
14
vasculature
1
mammary gland
Project
527
AMP
7
T1D
2
community
Genome assembly (visualization)
414
hg19
355
GRCh38
Lab
498
AMP-T2D consortium
25
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
56
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
missing controlled_by
Audit category:
21
inconsistent control read length
2
inconsistent control run_type
1
inconsistent assembly
assay_title!
total RNA-seq
audit.NOT_COMPLIANT.category!
missing controlled_by
BIOSAMPLE
ASSAY
536 results
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ChIP-seq
ATAC-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
CRISPR genome editing followed by DNA sequencing
Capture-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
365
1
2
2
2
1
1
GM12878
60
1
EndoC_BH1
15
19
6
1
3
2
2
1
Panc1
13
1
1
smooth muscle cell of the coronary artery
6
8
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