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Citing CMDGA
Experiment Matrix
Click or enter search terms to filter the experiments included in the matrix.
Assay
484
ChIP-seq
113
total RNA-seq
6
MeRIP-seq
6
pCHi-C
5
STARR-seq
4
Hi-C
CRISPR genome editing followed by DNA sequencing
2
Capture-C
2
HiChIP
1
WGBS
1
whole genome sequencing assay
Assay category
484
DNA binding
113
Transcription
DNA accessibility
4
3D chromatin structure
1
DNA methylation
1
DNA sequencing
Target of assay
361
transcription factor
89
recombinant protein
83
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
87
February, 2021
61
November, 2018
44
August, 2021
28
December, 2018
28
October, 2019
23
January, 2019
15
November, 2019
9
March, 2020
6
November, 2020
5
May, 2021
2
February, 2023
1
May, 2020
Available data
570
bam
517
bigWig
427
fastq
392
bed narrowPeak
353
bigBed narrowPeak
118
tsv
58
bed broadPeak
58
bigBed broadPeak
20
tagAlign
3
tar
2
bed bed3+
2
bedpe bed3+
2
hic
1
bed bedMethyl
1
bigBed bedMethyl
1
hdf5
1
vcf
Organism
624
Homo sapiens
Biosample type
2276
tissue
800
primary cell
624
cell line
351
in vitro differentiated cells
8
stem cell
Organ
400
liver
71
pancreas
60
blood
60
bodily fluid
58
artery
58
blood vessel
58
epithelium
58
heart
58
vasculature
18
kidney
8
embryo
1
mammary gland
Project
618
AMP
6
T1D
Genome assembly (visualization)
515
hg19
452
GRCh38
Lab
582
AMP-T2D consortium
34
Bing Ren, UCSD
6
Rohit N. Kulkarni, M.D., Ph.D.
2
Kyle Gaulton, UCSD
Audit category:
73
inconsistent ontology term
1
inconsistent control
Audit category:
13
missing controlled_by
Audit category:
26
inconsistent control read length
8
inconsistent control run_type
1
inconsistent assembly
assay_slims!
DNA accessibility
assay_title!
CRISPR genome editing followed by DNA sequencing
organ_slims!
spleen
BIOSAMPLE
ASSAY
624 results
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ChIP-seq
total RNA-seq
MeRIP-seq
pCHi-C
STARR-seq
Hi-C
Capture-C
HiChIP
WGBS
whole genome sequencing assay
cell line
HepG2
378
14
2
2
2
1
1
GM12878
60
EndoC_BH1
15
33
6
1
2
2
smooth muscle cell of the coronary artery
6
52
Panc1
13
1
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