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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
478
ChIP-seq
61
total RNA-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
3
CRISPR genome editing followed by DNA sequencing
3
Hi-C
2
Capture-C
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
478
DNA binding
63
Transcription
DNA accessibility
3
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
19
broad histone mark
19
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
November, 2018
44
August, 2021
29
February, 2021
28
December, 2018
27
October, 2019
23
January, 2019
15
November, 2019
9
March, 2020
6
February, 2023
6
November, 2020
5
May, 2021
2
March, 2023
1
May, 2020
1
October, 2022
Available data
512
bam
460
bigWig
427
fastq
388
bed narrowPeak
353
bigBed narrowPeak
66
tsv
58
bed broadPeak
58
bigBed broadPeak
14
tagAlign
3
tar
2
bedpe bed3+
2
hic
1
bed bed3+
1
bed bedMethyl
1
bigBed bedMethyl
1
txt
1
vcf
Organism
568
Homo sapiens
Biosample type
2234
tissue
796
primary cell
572
cell line
351
in vitro differentiated cells
10
stem cell
Organ
400
liver
71
pancreas
60
blood
60
bodily fluid
59
epithelium
artery
58
blood vessel
58
heart
58
vasculature
18
kidney
8
embryo
1
mammary gland
Project
561
AMP
9
T1D
2
community
Genome assembly (visualization)
458
hg19
395
GRCh38
Lab
525
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
73
inconsistent ontology term
1
inconsistent control
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
inconsistent assembly
assay_slims!
DNA accessibility
audit.WARNING.category!
inconsistent assembly
organ_slims!
artery
BIOSAMPLE
ASSAY
572 results
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ChIP-seq
total RNA-seq
MeRIP-seq
pCHi-C
STARR-seq
CRISPR genome editing followed by DNA sequencing
Hi-C
Capture-C
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
whole genome sequencing assay
cell line
HepG2
378
14
2
2
2
1
1
EndoC_BH1
15
33
6
3
1
2
2
1
GM12878
60
Panc1
13
H1-hESC
8
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