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| Status |
Public on Jul 08, 2019 |
| Title |
XG25 SCL-exo |
| Sample type |
SRA |
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| Source name |
MM cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell type: immortalized tumor plasma cells
cell line: XG25
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| Growth protocol |
XG21 and XG25 cell lines were cultured in RPMI 1640 medium, 10% fetal calf serum, and 2 ng/mL Interleukin-6.
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| 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).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
Library strategy: SCL-exo-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
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| Submission date |
Dec 20, 2018 |
| Last update date |
Jul 08, 2019 |
| Contact name |
Gilles Salbert |
| Organization name |
University Rennes 1
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| Department |
IGDR UMR6290
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| Street address |
263 Av. Gal. Leclerc
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| City |
Rennes |
| ZIP/Postal code |
35200 |
| Country |
France |
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| Platform ID |
GPL18460 |
| Series (1) |
| GSE124188 |
Genome-wide identification of 5hmCpGs in multiple myeloma |
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| Relations |
| BioSample |
SAMN10620471 |
| SRA |
SRX5170091 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3523607_XG25_SCL.wig.gz |
81.7 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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