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| Status |
Public on Nov 17, 2016 |
| Title |
NCD 2 |
| Sample type |
SRA |
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| Source name |
liver_NCD
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
tissue: liver
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| Treatment protocol |
Rats of the NCD group were treated normal drinking water for 21 weeks, rats of NCD+0.05%Pb group were exposed to 0.05% dosages of lead acetate through drinking water for 21 weeks
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| Growth protocol |
8-week-old Wistar rats were purchased from SLAC Laboratories, SIBS, Shanghai, China. Animals were housed at an ambient temperature of 22 ± 2∘C and maintained under a normal 12 hours light/dark cycle and allowed access to normal chow diet food ad libitum.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Livers were sampled, flash frozen in liquid nitrogen, and Genomic DNA was isolated and purified from 25 mg of frozen liver tissue with the DNeasy Tissue Kit (Qiagen, Germany, cat. no. 51306) .
Libraries were prepared according to Illumina's instructions. Breifly,Genomic DNA was isolated and purified from 25 mg of frozen liver tissue with the DNeasy Tissue Kit (Qiagen, Germany, cat. no. 51306).3ug of genomic DNA were broken into fragments by Covaris S2 system (Covaris, MA) for 52 seconds with 20% duty cycle, level 5 intensity and 200 cycles per burst. Fragmented DNA were purified by Ampure XP Beads (Beckman Coulter, CA) and the fragments were end-repaired, and a single A nucleotide was added to the 3' ends of the fragments in preparation for ligation to a methylated adapter (Illumina, CA) with a single-base T overhang. The ligation products were purified and size-selected (300-400bp) using agarose gel electrophoresis (Qiagen Minelute Gel Extraction Kit). DNA was modified with sodium bisulfite to convert unmethylated cytosine to uracil using the Zymo Gold methylation kit (Zymo Research, CA) according to the manufacturer's protocol and then purified. The purified converted DNA was amplified with PfuTurbo Cx Hotstart DNA Polymerase (Agilent Technologies, CA) and was purified again using AMPure XP beads. Library quality was monitored using the Agilent 2100 Bio-Analyzer (Agilent) and KAPA Library Quantification Kit (Kapa Biosystem). Paired-end sequencing (2×100 bp) was then carried out using the Illumina Hi-Seq 2000.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using the methylation-aware mapper bismark (version 0.13.0).
Samtools (version 0.1.19) was used to sort SAM files produced by bismark and de-duplicate reads.
SAM files were analyzed using the Bismark_methylation_extractor which was a subroutine of the methylation-aware mapper bismark (version 0.13.0)
Differential methylation was defined as a Fisher test correct p-value which was less than 0.01 for the type of CG and less than 0.05 for the type CHG and CHH(H was dedined as A,T or C) .
Genome_build: ftp://ftp.ensembl.org/pub/release-84/fasta/rattus_norvegicus/dna/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz
Supplementary_files_format_and_content: bigwig files include Methlation levels for each Sample
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| Submission date |
Nov 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sun hong ling |
| E-mail(s) |
[email protected]
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| Phone |
15000027837
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| Organization name |
Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine
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| Department |
Institute and Department of Endocrinology and Metabolism
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| Lab |
he lab of Endocrinology and Metabolism
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| Street address |
No.639 Zhizaoju Raod , Shanghai
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| City |
Shanghai |
| ZIP/Postal code |
200011 |
| Country |
China |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE89919 |
Whole Genome Bisulfite sequencing for liver DNA methylation analysis of rat exposed to 0.05% Pb |
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| Relations |
| BioSample |
SAMN06020504 |
| SRA |
SRX2352923 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2393203_Sample_Control2.mCHG.Bigwig |
274.4 Mb |
(ftp)(http) |
BIGWIG |
| GSM2393203_Sample_Control2.mCHH.Bigwig |
899.0 Mb |
(ftp)(http) |
BIGWIG |
| GSM2393203_Sample_Control2.mCpG.Bigwig |
265.3 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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