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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
3
Hi-C
2
ATAC-seq
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
453
DNA binding
27
Transcription
3
3D chromatin structure
2
DNA accessibility
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
15
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
452
bam
427
fastq
406
bigWig
369
bed narrowPeak
353
bigBed narrowPeak
58
bed broadPeak
58
bigBed broadPeak
28
tsv
14
tagAlign
3
tar
2
bed bed3+
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
1
vcf
Organism
498
Homo sapiens
Biosample type
2222
tissue
1001
primary cell
502
cell line
277
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
3
kidney
2
epithelium
1
mammary gland
Project
495
AMP
5
T1D
2
community
Genome assembly (visualization)
404
hg19
341
GRCh38
Lab
462
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
1
inconsistent assembly
assay_title!
DNase-seq
audit.ERROR.category!
inconsistent ontology term
lab.title!
Stephen Parker, UMich
organ_slims!
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BIOSAMPLE
ASSAY
502 results
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Clear Filters
ChIP-seq
total RNA-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
ATAC-seq
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
1
GM12878
60
1
Panc1
13
1
H1-hESC
8
EndoC_BH1
3
2
1
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