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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 08, 2012 |
| Title |
RRBS hematopoietic progenitor cells CD34_010611 |
| Sample type |
SRA |
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| Source name |
Peripheral blood after G-CSF stimulation
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| Organism |
Homo sapiens |
| Characteristics |
disease state: Healthy donor cells
Sex: m
age: 26
sample pairs: Promyelocte_060611
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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 |
GPL15456 |
| 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 |
SRX203029 |
| BioSample |
SAMN01801776 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1031212_CD34_010611.cpgs.txt.gz |
11.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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