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Sample GSM2473296 Query DataSets for GSM2473296
Status Public on Mar 17, 2017
Title LNCaP_Bis_rep2
Sample type SRA
Source name LNCaP cell line DNA
Organism Homo sapiens
Characteristics tissue type: LNCaP clone
passage: 73
Treatment protocol no treatment
Growth protocol Adult Brain Frontal Lobe genomic DNA from a single donor was purchased from Banksia Scientific Company (Bulimba, Australia, cat no D1234035). LNCaP cells were cultured as desribed previously [Song JZ et al, Oncogene 2002, 21:1048-1061].
Extracted molecule genomic DNA
Extraction protocol Genomic DNA from LNCaP cells was exctracted using QIAamp DNA Mini kit (Qiagen, USA)
CEGX TrueMethyl® WG
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model HiSeq X Ten
Description LNCaP clone FGC(ATCC® CRL-1740™). Androgen-sensitive human prostate adenocarcinoma cells derived from metastatic site: left supraclavicular lymph node
Data processing Bisulphite reads were aligned to the human genome using version 1.2 of an internally developed pipeline, publicly available for download from
Adaptor sequences and poor quality bases were removed using Trimgalore (version 0.2.8, in paired-end mode with default parameters.
Bismark v0.8.326 was then used to align reads to hg19 using the parameters “-p 4 –bowtie2 –X 1000 –unmapped –ambiguous –gzip –bam”
PCR duplicates were removed using Picard v1.91 (
Count tables of the number of methylated and unmethylated bases sequenced at each CpG site in the genome were constructed using bismark_methylation_extractor with the parameters “-p –no_overlap –ignore_r2 4 –comprehensive –merge_non_CpG –bedgraph –counts –report –gzip –buffer_size 20G”
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited
Submission date Jan 31, 2017
Last update date May 15, 2019
Contact name Ksenia Skvortsova
Phone 478135210
Organization name Garvan Institute
Department Genomics and Epigenetics
Lab Developmental Epigenomics
Street address 384 Victoria St, Darlinghurst
City Sydney
State/province NSW
ZIP/Postal code 2010
Country Australia
Platform ID GPL20795
Series (2)
GSE94331 Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA [BiSulfite-seq]
GSE94368 Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA
BioSample SAMN06285122
SRA SRX2529940

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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