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| Status |
Public on Aug 12, 2014 |
| Title |
93A |
| Sample type |
SRA |
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| Source name |
Atherosclerotic lesion
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| Organism |
Homo sapiens |
| Characteristics |
disease state: Diseased
tissue: carotid tissue
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| Treatment protocol |
Fresh frozen in RNAlater (Ambion)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)
BS-seq library constructing, 10ug genomic DNA was fragmented using a Covaris sonication system (Covaris S2). Following fragmentation, libraries were constructed using the Illumina Paired-End protocol consisting of end repair, <A> base addition and methylated-adaptor ligation. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO). Different insert size were excised from the same lane of a 2% TAE agarose gel. Normally, three bands are excised corresponding to DNA insert sizes of 80-100 bp, 100-120 bp to 120-150bp. Products were purified by using QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. PCR was carried out in a final reaction volume of 50ul consisting of 20ul purified DNA, 4ul 2.5 mM dNTP, 5 ul 10X buffer, 0.5 ul JumpStart Taq DNA polymerase, 2ul 10uM PCR primers and 37.5 ul ÎœltraPure TM Water and the following thermal cycling program: 94C 30 s, 10 cycles of 94C 30 s, 60C 30 s, 72C 30 s then prolong with 1 min at 72C. PCR products were sequenced with an Illumina genome analyzer. The reads generated by Illumina sequencing were aligned to the reference genome using SOAPaligner2. The alignment and methylation estimation was performed as described before (Li, Y. et al. PLoS Biol 8, e1000533 (2010)).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava1.7 software used for basecalling
Read mapping: Rtwo reference sequences were prepared based on the HG19 reference genome
The alignment was performed using the bowtie alignment software version 0.12.8
methylation calls files for C's in the bowtie alignment files were generated using Bismarck software
Genome_build: HG19
Supplementary_files_format_and_content: methylation calls files. Columns are : chromosome, position, methylated, unmethylated
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| Submission date |
Apr 23, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Manel Esteller |
| Organization name |
IDIBELL
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| Department |
PEBC
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| Lab |
Cancer Epigenetics
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| Street address |
Hospital Duran i Reynals Av. Gran Via s/n km, 2.7
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| City |
L'Hospitalet de Llobregat |
| State/province |
Barcelona |
| ZIP/Postal code |
08908 |
| Country |
Spain |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE46327 |
Genome-wide DNA methylation aberrations in human atherosclerosis (sequencing) |
| GSE46401 |
Genome-wide DNA methylation aberrations in human atherosclerosis |
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| Relations |
| BioSample |
SAMN02055560 |
| SRA |
SRX271441 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1128658_CpG_context_93A.sam.sorted.pileup.txt.gz |
210.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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