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Schema
Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
465
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
465
DNA binding
63
Transcription
23
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
345
transcription factor
88
recombinant protein
81
control
63
RNA binding protein
37
histone
37
histone modification
24
chromatin remodeller
19
broad histone mark
18
narrow histone mark
3
nucleotide modification
2
other context
2
other post-translational modification
Date released
305
November, 2017
58
November, 2018
44
August, 2021
30
February, 2021
30
October, 2019
28
December, 2018
23
January, 2019
21
May, 2021
16
November, 2019
11
March, 2020
6
February, 2023
6
November, 2020
2
March, 2023
1
January, 2018
1
May, 2020
1
October, 2022
Available data
503
bam
454
bigWig
414
fastq
380
bed narrowPeak
343
bigBed narrowPeak
67
tsv
59
bed broadPeak
59
bigBed broadPeak
14
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
579
Homo sapiens
Biosample type
2429
tissue
1000
primary cell
583
cell line
385
in vitro differentiated cells
10
stem cell
Organ
388
liver
92
pancreas
79
epithelium
66
artery
66
blood vessel
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
572
AMP
9
T1D
2
community
Genome assembly (visualization)
454
hg19
395
GRCh38
Lab
536
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:
92
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
audit.ERROR.category!
audit script error
organ_slims!
heart
audit.NOT_COMPLIANT.category!
missing controlled_by
BIOSAMPLE
ASSAY
583 results
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Clear Filters
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
365
14
1
2
2
2
1
1
EndoC_BH1
15
33
19
6
1
3
2
2
1
GM12878
60
1
Panc1
13
1
1
H1-hESC
8
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