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Status |
Public on Nov 08, 2012 |
Title |
RRBS PML-RARa Knock-in mice mm_33_PML-RAR_gr1 |
Sample type |
SRA |
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Source name |
Gr1+ sorted mouse bone marrow
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Organism |
Mus musculus |
Characteristics |
disease state: Gr1+ bone marrow strain: C57BL6 genotype/variation: PML-RARa (+/-) Sex: f age: 6-months pre-leukemic
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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 5mC-methylated Illumina paired end sequencing adapters (Illumina Inc., San Diego, CA). Fragments in a range of 40 to 220 bps insert size were gel-purified (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). Each library was sequenced on a separate lane using an Illumina HiScanSQ instrument with version 2.5 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 |
RANDOM |
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 Off-Line Basecaller (OLB) was used for bcl to qseq conversion Illumina paired-end adapter sequences were removed using Cutadapt version 0.9.3 Reads were mapped using Bismark version 0.5 Methylation calls from Bismark were extracted with a modified methylation_extractor script which removed 3’-MspI-sites The extracted methylation data was further analyzed in R/Bioconductor with the BiSeq package Genome_build: hg19 for human samples and mm9 for mouse samples Supplementary_files_format_and_content: Extracted CpG methylation call files were generated using R/Bioconductor with help of the BiSeq package. 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 |
Nov 05, 2012 |
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) |
GSE42044 |
DNA methylation changes are a late event in Acute Promyelocytic Leukemia and coincide with loss of transcription factor binding (sequencing) |
GSE42119 |
DNA methylation changes are a late event in Acute Promyelocytic Leukemia and coincide with loss of transcription factor binding |
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Relations |
SRA |
SRX203050 |
BioSample |
SAMN01801797 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1031233_mm_33_PML-RAR_gr1.cpgs.txt.gz |
7.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Processed data provided as supplementary file |
Raw data are available in SRA |
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