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| Status |
Public on Dec 18, 2013 |
| Title |
H3R_d0_rep1 |
| Sample type |
SRA |
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| Source name |
RRBS highly metastatic HTB56 cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HTB56
rounds of in vivo selection: 3
5-azacytidine status: untreated
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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
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
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 |
Feb 19, 2013 |
| 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) |
| GSE44390 |
DNA Methyltransferase inhibition reverses epigenetically embedded phenotypes in lung cancer preferentially affecting Polycomb target genes |
| GSE52140 |
Examination of genome-wide methylation changes in lung cancer cell lines A549 (A) and HTB56 (H) [RRBS-Seq experiments] |
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| Relations |
| BioSample |
SAMN01923884 |
| SRA |
SRX381433 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1084245_H3R_d0_rep1.cpgs.txt.gz |
15.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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