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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 31, 2021 |
| Title |
NK |
| Sample type |
SRA |
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| Source name |
Natural killer cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Innate lymphoid cells
tissue: lymph node
marker: CD3-CD19-CD127-NK1.1+T-bet+
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lymph nodes were removed and meshed through a sieve. Genomic DNA was prepared from ILC subpopulations sorted by FACS. Genomic DNA was converted by bisulfite and subjected to library preparation.
The bislufite converted DNA was fragmented by sonication and served as input for library preparation by using the Accel-NGS Methyl-Seq DNA Library Kit.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Illumina RTA3 was used for basecalling.
All libraries have been assessed for sufficient sequencing quality and potential adapter contamination using programs FastQC (Babraham Bioinformatics; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), trim_galore and cutadapt. To avoid potential methylation bias due to insufficient end-repair reaction, from both reads (R1/R2) the first 10 bases at the 5' as well as the 3' end have been trimmed after adapter removal and trimming of low-quality ends with a Phred score below 20. Reads, which are shorter than 20 nucleotides after trimming have been discarded.
Quality controlled libraries have been mapped against the mouse reference genome (version: GRCm38, w/o gonosomes) using the bisulfite short read mapping software BSMAP. In order to accurately measure the methylation levels of cytosines inside CpG context genome-wide and obtain corresponding coverage information, methylation level calling has taken only properly paired unique read pair mappings (methratio.py parameters: --unique, --paired,--remove-duplicate) into account.
The reliable detection of DMRs even in the absence of replicates was performed with the software tool metilene. We considered for the detection process only CpG motifs with a coverage of at least five that are present in at least one sample. In addition, a DMR has to contain at least three CpG's with a distance between two CpGs of at most 200 nucleotides and a total length of the region of at least 300. Further on, to be classified as DMR, the difference in mean methylation (i.e., mean over all CpG's of a region) of a region between two compared samples/conditions has to be greater or equal 25 percent and the adjusted P-value from the 2D-KS test has to be at most 0.1
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: *,methout.txt: CSV formatted file with methylation values for all CpGs for each sample as generated by BSMAp/methratio.py; *metilene_DMRs.csv.gz: Differentially methylated regions for each pairwise comparison (generated by metilene)
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| Submission date |
Mar 03, 2021 |
| Last update date |
May 31, 2021 |
| Contact name |
Michael Beckstette |
| Organization name |
Helmholtz Centre for Infection Research
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| Department |
Molecular Infection Biology
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| Lab |
Experimental Immunology
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| Street address |
Inhoffenstrase 7
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| City |
Braunschweig |
| State/province |
Lower Saxony |
| ZIP/Postal code |
38124 |
| Country |
Germany |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE168209 |
Genome-wide methylation analysis of murine innate lymphoid cells |
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| Relations |
| BioSample |
SAMN18133197 |
| SRA |
SRX10235070 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5133979_NK1-1_S58_L00X_R1_001_val_1_NK1-1_S58_L00X_R2_001_val_2.methout.txt.gz |
272.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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