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| Status |
Public on Mar 03, 2015 |
| Title |
RRBS F3D7 |
| Sample type |
SRA |
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| Source name |
C57Bl/6 Mouse
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| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
generation: F3
agent: decitabine
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
100 ng of DNA was used for RRBS library preparation using a published protocol with minor modifications (Smith et al, 2009). Briefly, genomic DNA was digested with MspI (NEB, Ipswich, MA, USA) end-repaired and A-tailed with the Klenow-fragment enzyme (NEB), and ligated (NEB) with Illumina TruSeq adapters (Illumina Inc., San Diego, CA). Fragments in a range of 40 to 280 bps insert size were purified from a SYBR gold (Invitrogen) pre-stained agarose gel (NuSieve 3:1 Agarose, Lonza, Allenda, NJ, USA). Libraries were bisulfite converted using the EZ DNA Methylation™ Kit (ZymoResearch, Irvine, CA, USA) and amplified using PfuTurboCx polymerase (Agilent, Santa Clara, CA, USA). The libraries were sequenced on an Illumina HiScanSQ instrument with version 3 sequencing chemistry. Libraries were spiked with 45% PhiX DNA to counteract the imbalance in nucleotide representation.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiScanSQ |
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| Data processing |
Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina HiScan-SQ
CASAVA version 1.8.2 was used to export raw sequencing data in fastq format.
Illumina paired-end adapter sequences were removed using Trim Galore! version 0.3.3 with implemented Cutadapt version 1.1
Reads were mapped using Bismark version 0.10.1
Methylation calls from Bismark were extracted the Bismark methylation_extractor script
The extracted methylation data was further compiled using a custom R script
Genome_build: mm10
Supplementary_files_format_and_content: Each processed file contains a column for chromosome, position and extracted methylation data for the respective sample. For each CpG position observed the number of methylated / unmethylated reads is listed.
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| Submission date |
Jul 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Christian Rohde |
| E-mail(s) |
christian.rohde@uni-heidelberg.de
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| Organization name |
Heidelberg University
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| Lab |
Molecular Hematology and Oncology
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| Street address |
Im Neuenheimer Feld 410
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| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
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| Platform ID |
GPL16173 |
| Series (1) |
| GSE59575 |
Direct but No Transgenerational Effects of Decitabine and Vorinostat on Male Fertility |
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| Relations |
| BioSample |
SAMN02927297 |
| SRA |
SRX657199 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1439621_F3D7.cpgs.txt.gz |
7.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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