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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 15, 2018 |
| Title |
Control Liver_Alb-R26Met |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
strain: 50% mixed 129/SV and C57BL6
tissue: Liver
age: 71 weeks
genotype: wild type
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Control livers and tumors were disected and DNA was extracted from each individual sample using Phenol-chloroform protocol. Then, genomic DNA was used to analyze the DNA methylation profile by the EpiQuest™ Genome-Wide Full Service (Zymo Research Company). This included sample standardization, library preparation, bisulfite conversion, next-generation bisulfite sequencing, and bioinformatics pipeline.
Libraries were prepared from 200-500ng of genomic DNA digested with 60 units of TaqαI and 30 units of MspI (NEB) sequentially and then extracted with Zymo Research DNA Clean and Concentrator™-5 kit (Cat#: D4003). Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines (www.illumina.com). Adaptor-ligated fragments of 150–250bp and 250–350bp in size were recovered from a 2.5% NuSieve 1:1 agarose gel (Zymoclean™ Gel DNA Recovery Kit, Zymo Research Cat#: D4001). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning™ Kit (Zymo Research, Cat#: D5020). Preparative-scale PCR was performed and the resulting products were purified (DNA Clean and Concentrator™ - Zymo Research, Cat#D4005) for sequencing on an Illumina HiSeq.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
Sequence reads from bisulfite-treated EpiQuest libraries were identified using standard Illumina base-calling software and then analyzed using a Zymo Research proprietary analysis pipeline, which is written in Python and used Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) to perform the alignment. Index files were constructed using the bismark_genome_preparation command and the entire reference genome. The --non_directional parameter was applied while running Bismark. All other parameters were set to default. Filled-in nucleotides were trimmed off when doing methylation calling. The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T.
Genome_build: mm9
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| Submission date |
Nov 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Daian Fabrice |
| E-mail(s) |
fabrice.daian@univ-amu.fr
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| Organization name |
CNRS
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| Department |
UMR7288
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| Lab |
IBDM
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| Street address |
Case 907 - Parc Scientifique de Luminy
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| City |
Marseille |
| ZIP/Postal code |
13288 |
| Country |
France |
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| Platform ID |
GPL18480 |
| Series (1) |
| GSE90093 |
Reprogramming oncogene levels through gene body hypermethylation in RTK-driven cancer |
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| Relations |
| BioSample |
SAMN06043969 |
| SRA |
SRX2364129 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2397575_RRBS_cpgMethylation_zr274_14.RRBS.bed.gz |
22.7 Mb |
(ftp)(http) |
BED |
| GSM2397575_RRBS_cpgReads_zr274_14.RRBS.bed.gz |
36.4 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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