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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
446
ChIP-seq
77
total RNA-seq
10
ATAC-seq
4
STARR-seq
4
pCHi-C
3
CRISPR genome editing followed by DNA sequencing
3
Hi-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
Assay category
446
DNA binding
79
Transcription
12
DNA accessibility
3
3D chromatin structure
1
DNA methylation
DNA sequencing
Target of assay
341
transcription factor
81
recombinant protein
75
control
62
RNA binding protein
25
histone
25
histone modification
24
chromatin remodeller
13
broad histone mark
12
narrow histone mark
2
other context
2
other post-translational modification
Date released
305
November, 2017
70
February, 2021
58
November, 2018
40
August, 2021
28
December, 2018
23
January, 2019
17
October, 2019
6
February, 2023
4
March, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
507
bam
452
bigWig
414
fastq
371
bed narrowPeak
343
bigBed narrowPeak
80
tsv
59
bed broadPeak
59
bigBed broadPeak
20
tagAlign
3
bed bed3+
3
tar
1
bed bed3
1
bed bedMethyl
1
bedpe bed3+
1
bigBed bedMethyl
1
hdf5
1
hic
1
txt
Organism
552
Homo sapiens
Biosample type
2660
tissue
990
primary cell
556
cell line
273
in vitro differentiated cells
9
stem cell
Organ
387
liver
66
artery
66
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
16
pancreas
8
embryo
4
kidney
3
epithelium
1
mammary gland
Project
549
AMP
5
T1D
2
community
Genome assembly (visualization)
458
hg19
402
GRCh38
Lab
517
AMP-T2D consortium
32
Bing Ren, UCSD
5
Kyle Gaulton, UCSD
2
Anna Gloyn, Oxford
Audit category:
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_slims!
DNA sequencing
audit.ERROR.category!
inconsistent ontology term
audit.NOT_COMPLIANT.category!
missing controlled_by
BIOSAMPLE
ASSAY
556 results
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Clear Filters
ChIP-seq
total RNA-seq
ATAC-seq
STARR-seq
pCHi-C
CRISPR genome editing followed by DNA sequencing
Hi-C
DNase-seq
HiChIP
CRISPR genome editing followed by sgRNA sequencing
MPRA
WGBS
shRNA RNA-seq
siRNA RNA-seq
cell line
HepG2
365
14
1
2
2
2
1
smooth muscle cell of the coronary artery
6
52
8
GM12878
60
1
Panc1
13
1
1
H1-hESC
8
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