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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
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
WGBS
1
whole genome sequencing assay
Assay category
478
DNA binding
61
Transcription
23
DNA accessibility
4
3D chromatin structure
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
60
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
November, 2020
5
February, 2023
1
January, 2018
1
May, 2020
Available data
515
bam
465
bigWig
426
fastq
392
bed narrowPeak
355
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
hdf5
1
vcf
Organism
591
Homo sapiens
Biosample type
2610
tissue
1010
primary cell
591
cell line
394
in vitro differentiated cells
8
stem cell
Organ
400
liver
91
pancreas
78
epithelium
66
artery
blood vessel
66
heart
66
vasculature
61
blood
61
bodily fluid
19
kidney
8
embryo
1
mammary gland
Project
582
AMP
9
T1D
Genome assembly (visualization)
466
hg19
399
GRCh38
Lab
546
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
5
Kyle Gaulton, UCSD
Audit category:
92
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
organ_slims!
blood vessel
assay_title!
WGBS
BIOSAMPLE
ASSAY
591 results
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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
whole genome sequencing assay
cell line
HepG2
378
14
1
2
2
2
1
EndoC_BH1
15
33
19
6
1
3
2
2
GM12878
60
1
Panc1
13
1
1
H1-hESC
8
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