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Sample GSM3523608 Query DataSets for GSM3523608
Status Public on Jul 08, 2019
Title MM35174 SCL
Sample type SRA
 
Source name primary MM cells
Organism Homo sapiens
Characteristics cell type: tumor plasma cells
Growth protocol XG21 and XG25 cell lines were cultured in RPMI 1640 medium, 10% fetal calf serum, and 2 ng/mL Interleukin-6.
Extracted molecule genomic DNA
Extraction protocol MM cells were purified from bone marrow samples using anti-CD138 MACS microbeads (Miltenyi Biotech). Genomic DNA was extracted using a DNeasy Blood and Tissue kit (Qiagen, France).
Ten micrograms of genomic DNA from MM patients or cell lines were subjected to the SCL-exo protocol (Sérandour et al., Genome Biol, 2016). Libraries were obtained using the TruSeq ChIP Sample Prep Kit from Illumina and quantified using the KAPA library quantification kit (KAPA Biosystems). Libraries were sequenced (50bp, single end) with HiSeq 1500 (Illumina).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 1500
 
Data processing Library strategy: SCL-seq
SCL-exo fastq files were filtered using SolexaQA to retain high-quality reads only (Q=20, l=17) before being mapped to hg19 genome assembly, forward and reverse strands separately, using Bowtie with parameters l=32 bp, n=1, m=1, strata, best, and Samtools.
The bam files were then processed to generate .wig files using MACS 1.4.0.
SCL-exo data reads for which a single CpG was found within 10 bases from their 5’ end were selected to build a single-CpG resolution .wig file in which signal at identified CpGs corresponds to the sum of the reads covering both Cs (two strands) at each given CpG.
Genome_build: hg19
Supplementary_files_format_and_content: wig files
 
Submission date Dec 20, 2018
Last update date Jul 08, 2019
Contact name Gilles Salbert
Organization name University Rennes 1
Department IGDR UMR6290
Street address 263 Av. Gal. Leclerc
City Rennes
ZIP/Postal code 35200
Country France
 
Platform ID GPL18460
Series (1)
GSE124188 Genome-wide identification of 5hmCpGs in multiple myeloma
Relations
BioSample SAMN10620470
SRA SRX5170092

Supplementary file Size Download File type/resource
GSM3523608_MM35174_SCL.wig.gz 110.5 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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