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| Status |
Public on Mar 03, 2022 |
| Title |
WGBS_MUTZ5 |
| Sample type |
SRA |
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| Source name |
MUTZ5 B-ALL cell line
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| Organism |
Homo sapiens |
| Characteristics |
condition: WT
cell line: MUTZ5
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| Growth protocol |
ALL cell lines were maintained in RPMI 1640 medium containing 10% or 20% fetal bovine serum (HyClone), penicillin/streptomycin (100 U/mL), and glutamine (100 µM) at 37°C, 5% CO2. Cell identity was confirmed by short tandem repeat (STR) profiling using a PowerPlex Fusion System (Promega). All of the cell lines were confirmed as Mycoplasma spp. free using the Universal Mycoplasma Detection Kit (American Type Culture Collection, Manassas, VA).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells at exponential growth phase were spun down at 1500 rpm for 3 minutes and cell pellet was used to extract genomic DNA.
Whole genome bisulfite sequencing was performed on bisulfite-modified DNA-sequencing library generated according to Illumina’s instructions accompanying the TruSeq DNA Methylation Kit (Part# EGMK81312). 200ng of genomic DNA, including 0.2% Lambda DNA (N6-methyladenine-free; NEB) was bisulfite converted in a single reaction using the EZ DNA Methylation Gold Kit (Zymo Research) as outlined by the manufacturer. The bisulfite converted DNA (bsDNA) was split into four aliquots per sample. Four single indexed WGBS libraries were constructed with the EpiGnome Methyl-Seq kit (EGMK81312, Epicentre) according to the manufacturer’s recommendations. The final concentration of each library was accurately determined through qPCR (KAPA Biosystems). The four independent libraries were normalized, pooled, and loaded across three lanes of the HiSeq 2000 instrument (Illumina).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Whole genome bisulfite sequencing
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| Data processing |
Paired-end reads from sequencing were trimmed using trimgalore (v0.4.4, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), removing low quality (Q30) bases and adapter sequences, and clipping 10 bases from each end of the read pairs.
Trimmed reads were then mapped to hg19 using BSMAP (v2.90) with default parameters to report unique pairs with a 17 base pair minimal insert size and 600 base pair maximum insert size
Duplicates were removed using the ‘MarkDuplicates’ command from GATK (version 4.1.4.1; --VALIDATION_STRINGENCY=LENIENT --REMOVE_DUPLICATES=true).
Methylation rates were called using mcall from the MOABS package (version 1.3.2; default parameters).
Only CpGs covered by at least 10 reads were considered for downstream analyses.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph file containing methylation rates for CpGs covered by at least 10 reads: <chr> <start> <end> <methylation rate>
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| Submission date |
Jan 17, 2022 |
| Last update date |
Mar 03, 2022 |
| Contact name |
Sara Hetzel |
| E-mail(s) |
hetzel@molgen.mpg.de
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| Organization name |
Max Planck Institute for Molecular Genetics
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| Department |
Genome Regulation
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| Lab |
Meissner Lab
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| Street address |
Ihnestraße 63
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| City |
Berlin |
| ZIP/Postal code |
14195 |
| Country |
Germany |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE164040 |
Acute lymphoblastic leukemia displays a distinct highly methylated genome |
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| Relations |
| BioSample |
SAMN25042772 |
| SRA |
SRX13811036 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5821057_WGBS_MUTZ5_hg19.bed.gz |
167.2 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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