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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
61
total RNA-seq
21
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
459
DNA binding
63
Transcription
23
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
357
transcription factor
89
recombinant protein
81
control
65
RNA binding protein
38
histone
38
histone modification
30
chromatin remodeller
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
307
November, 2017
61
November, 2018
43
August, 2021
30
February, 2021
28
December, 2018
26
October, 2019
23
January, 2019
21
May, 2021
11
March, 2020
10
November, 2019
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
498
bam
448
bigWig
419
fastq
375
bed narrowPeak
345
bigBed narrowPeak
67
tsv
51
bed broadPeak
51
bigBed broadPeak
8
tagAlign
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
573
Homo sapiens
Biosample type
2218
tissue
953
primary cell
577
cell line
337
in vitro differentiated cells
9
stem cell
Organ
392
liver
82
pancreas
73
epithelium
66
artery
66
blood vessel
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
566
AMP
9
T1D
2
community
Genome assembly (visualization)
448
hg19
384
GRCh38
Lab
531
AMP-T2D consortium
33
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
86
inconsistent ontology term
1
inconsistent control
1
inconsistent replicate
Audit category:
13
missing controlled_by
Audit category:
20
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
target.investigated_as!
broad histone mark
organ_slims!
heart
BIOSAMPLE
ASSAY
577 results
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ChIP-seq
total RNA-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
369
14
1
2
2
2
1
1
EndoC_BH1
9
33
19
6
1
3
2
2
1
GM12878
60
1
Panc1
9
1
1
H1-hESC
8
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