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| Status |
Public on Sep 01, 2016 |
| Title |
shallow TABseq on a PyMT-induced breast tumor from a PHD2+/- mouse 1 |
| Sample type |
SRA |
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| Source name |
PyMT-induced breast tumor
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| Organism |
Mus musculus |
| Characteristics |
strain: FVB, Phd2+/-
hydrodynamically injected plasmid: NA
age: 16 weeks
replicate: A
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| Treatment protocol |
Mice were either WT or Phd heterozygotes, or hydrodynamically injected with an empty or sFlk1-overexpression plasmid. Whereas the Phd2+/-genotype restores vascularisation and oxygenation levels in the tumor, the latter treatment renders tumors more hypoxic
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| Growth protocol |
breast tumors were isolated, flash-frozen in liquid nitrogen and stored at -150 until further processing
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nucleic acids were subsequently extracted using the Wizard Genomic DNA Purification (Promega, Leiden, The Netherlands) kit according to instructions, with all buffers supplemented with DFO (200 µM), dissolved in 80 µL PBS-DFO with RNAse A (200 units, NEB, Ipswich, MA, USA), incubated for 10 minutes at 37°C. After proteinase K addition (200 units) and incubation for 30 minutes at 56°C, DNA was purified using the QIAQuick blood and tissue kit (all buffers supplemented with DFO), eluted in 100 µL of a 10 mM Tris, 1mM EDTA solution (pH 8) and stored at -80°C until further processing.
library preparations and TAB-conversion were as described by Yu and colleagues (Nat Protoc 2012), except that bisulfite conversion was done using the EZ DNA Methylation-Lightning Kit (ZYMO), and libraries were amplified using the KAPA Uracil+ 2x master mix.
tet-assisted-bisulfite-seq
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Sample 50
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| Data processing |
alignment was done using BisMark 0.13.1 (http://www.bioinformatics.babraham.ac.uk/projects/bismark/)
SeqMonk 0.29.0 was used to hydroxymethylation levels at 300kb sliding windows
Genome_build: Mm9
Supplementary_files_format_and_content: "TABseq hmC percentage in 300kb bins.txt" contains average 5hmC levels in 300kb bins for each sample
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| Submission date |
Jul 27, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Bernard thienpont |
| Organization name |
VIB
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| Department |
Vesalius Research Center
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| Lab |
Translational genetics
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| Street address |
Herestraat 49
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| City |
Heverlee |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE71402 |
Tumor hypoxia causes DNA hypermethylation by reducing TET activity (TAB-Seq) |
| GSE71403 |
Tumor hypoxia causes DNA hypermethylation by reducing TET activity |
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| Relations |
| BioSample |
SAMN03939976 |
| SRA |
SRX1121788 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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