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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
453
ChIP-seq
25
total RNA-seq
4
STARR-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
2
ATAC-seq
2
DNase-seq
2
Hi-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
453
DNA binding
27
Transcription
4
DNA accessibility
2
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
349
transcription factor
82
recombinant protein
73
control
64
RNA binding protein
30
chromatin remodeller
26
histone
26
histone modification
13
broad histone mark
13
narrow histone mark
2
other context
2
other post-translational modification
Date released
315
November, 2017
61
November, 2018
41
August, 2021
28
December, 2018
23
January, 2019
16
October, 2019
6
February, 2023
4
February, 2021
4
March, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
454
bam
427
fastq
407
bigWig
371
bed narrowPeak
355
bigBed narrowPeak
59
bed broadPeak
59
bigBed broadPeak
28
tsv
14
tagAlign
3
tar
2
bed bed3+
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hic
1
txt
1
vcf
Organism
499
Homo sapiens
Biosample type
2372
tissue
1025
primary cell
503
cell line
278
in vitro differentiated cells
9
stem cell
Organ
401
liver
66
artery
66
blood vessel
heart
66
vasculature
61
blood
61
bodily fluid
15
pancreas
8
embryo
4
kidney
3
epithelium
1
mammary gland
Project
496
AMP
5
T1D
2
community
Genome assembly (visualization)
405
hg19
342
GRCh38
Lab
463
AMP-T2D consortium
33
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
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
inconsistent assembly
audit.WARNING.category!
inconsistent assembly
organ_slims!
heart
audit.ERROR.category!
inconsistent ontology term
BIOSAMPLE
ASSAY
503 results
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Clear Filters
ChIP-seq
total RNA-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
ATAC-seq
DNase-seq
Hi-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
1
2
1
1
GM12878
60
1
Panc1
13
1
H1-hESC
8
EndoC_BH1
3
2
1
EndoC-BH1
1
1
HEK293T
2
early embryonic cell
2
glomerular visceral epithelial cell
1
1
iPSC derived cell line
2
MCF-7
1
MIN6
1
fibroblast cell line
1
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