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| Status |
Public on Jan 11, 2016 |
| Title |
RRBS MLL-AF9 c-kit+ leukemic spleen cells Dnmt3b-knockin MLL-AF9-85-0 |
| Sample type |
SRA |
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| Source name |
leukemic spleen
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| Organism |
Mus musculus |
| Characteristics |
cell type: MLL-AF9 c-kit+ leukemic spleen cells Dnmt3b-knockin
dnmt3b-knockin: Dnmt3b-knockin
oncogene: MLL-AF9
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
0.3 – 1 µg 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
Illumina CASAVA software was used to demultiplex and export reads in FASTQ format
Illumina paired-end adapter sequences and 3'-MspI-sites were removed with help of Trim Galore! version 0.2.2 using the default settings for RRBS data processing
Reads were mapped using Bismark version 0.7.4
Methylation calls were extracted with the Bismark methylation_extractor script
The extracted methylation data was further analyzed in R using methylKit, the Bioconductor BiSeq package and custom scripts
Genome_build: mm9
Supplementary_files_format_and_content: Extracted CpG methylation call files were generated using custom R scripts. 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 17, 2015 |
| 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 (2) |
| GSE71039 |
Increased DNA Methylation of Dnmt3b-Targets Impairs Leukemogenesis (RRBS) |
| GSE71041 |
Increased DNA Methylation of Dnmt3b-Targets Impairs Leukemogenesis |
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| Relations |
| BioSample |
SAMN03876680 |
| SRA |
SRX1100043 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1825970_MLL-AF9-85-0_cpgs.txt.gz |
13.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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