|
| Status |
Public on Nov 08, 2012 |
| Title |
TrueSeq RRBS APL_patient APL_patient_48ATRA |
| Sample type |
SRA |
| |
|
| Source name |
In-vitro ATRA treated APL blast
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: 48h ATRA treated APL blasts
Sex: m
age: 45
sample pairs: APL patient
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
TrueSeq RRBS: Briefly, 500 ng genomic DNA was digested with MspI, end-repaired and A-tailed with the Klenow-fragment enzyme, and then ligated with 5mC-methylated Illumina TruSeq adapters. We followed the general library preparation instructions from Illumina and purified fragments in a range of 40 to 220 bps insert size from a SYBR Gold prestained gel. Subsequently, the libraries were bisulfite converted using the EZ DNA Methylation™ Kit (ZymoResearch, Irvine, CA, USA). Next the Libraries were amplified using PfuTurboCx polymerase. Libraries were sequenced in a pool with other libraries using an Illumina HiScanSQ instrument with TruSeq SBS Kit v3 sequencing chemistry. After demultiplexing with the CASAVA 1.8.2 (Illumina), the reads were subject to the described standard analysis pipeline.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiScanSQ |
| |
|
| 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.
|
| |
|
| Submission date |
Nov 05, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Christian Rohde |
| E-mail(s) |
christian.rohde@uni-heidelberg.de
|
| Organization name |
Heidelberg University
|
| Lab |
Molecular Hematology and Oncology
|
| Street address |
Im Neuenheimer Feld 410
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| 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 |
|
| Relations |
| SRA |
SRX203043 |
| BioSample |
SAMN01801790 |
