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| Status |
Public on Jan 11, 2021 |
| Title |
5624_OXO |
| Sample type |
SRA |
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| Source name |
proximal colon
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| Organism |
Mus musculus |
| Characteristics |
strain: 129S6/SvEvTac-Rag2tm1FwIl10-/-
treatment: sterile media
gender: male
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| Treatment protocol |
Mice aged 6-7 weeks received two doses every other day of 0.2 mL of 2 x 108 fresh inoculums (infected group) or sterile media (control group).
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| Growth protocol |
129S6/SvEvTac-Rag2tm1FwIl10-/- (Rag2-/- / Il10-/-) mice were used and housed in an AAALAC-accredited specific pathogen-free barrier facility. Mice were maintained in polycarbonate microisolator caging (Allentown Caging Equipment Inc., Allentown, NJ) and provided pelleted diet (ProLab 3000, Purina Mills, St. Louis, MO) and filtered water ad libitum.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA, total RNA were extracted from approximately 10 mg of proximal colon tissue using AllPrep DNA/RNA mini kit (QIAGEN, Hilden, Germany).
RRBS and oxRRBS libraries were prepared by Ovation® RRBS Methyl-Seq with TrueMethyl® oxBS kit (Tecan, Redwood City, CA) according to the manufacturer’s instructions.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
NextSeq 550 |
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| Data processing |
Reduced representation bisulfite sequencing (RRBS) reads and oxRRBS reads were trimmed of low quality bases and adapter contamination with TrimGalore! 0.4.4_dev (http://www.bioinformatics. babraham.ac.uk/projects/trim_galore/) in paired-end mode, using Cutadapt version 1.8.1. (https://journal.embnet.org/index.php/embnetjournal/article/view/200). Any read pairs where one mate failed quality control were discarded.
Cleaned reads were aligned to the mouse mm10 genome with Bismark version 0.19.0. Resulting alignments were cleaned of PCR duplicates with NuDup (https://github.com/nugentechnologies/nudup), and reads with mapping quality of less than 20 were removed.
Analysis of methylated and hydroxymethylated regions followed the Methpipe analysis pipeline (commit 77d7728e6c52592a71706834d86f5e69183ef082 (Sept 7, 2018))
Genome-wide cytosines were filtered to represent only symmetrically methylated CpG sites. CpG sites that were not covered by at least 10 reads in each sample were discarded. CpG sites were further filtered to exclude sites that occurred within “blacklisted” regions of the mm10 genome assembly (ENCODE file ID ENCFF547MET).
Differentially methylated (DMR) and hydroxymethylated (DhMR) regions were identified by merging consecutive CpGs that crossed the threshold for statistical significance at a false discovery rate of 0.05, and filtering regions with at least three significant CpG sites.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data are output from the methcount in the meth pipe analysis, which contains the chromosome location of the CpG sites, fraction numbers of 5mC+5hmC(BS dataset) or 5mC(oxBS dataset) and the corresponding coverage in each CpG site.
Supplementary_files_format_and_content: BS:5mC+5hmC fraction table
Supplementary_files_format_and_content: OXO:5mC fraction table
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| Submission date |
Dec 11, 2020 |
| Last update date |
Jan 11, 2021 |
| Contact name |
Qiyuan Han |
| E-mail(s) |
hanxx963@umn.edu
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| Organization name |
University of Minnesota
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| Street address |
2231 6th St. Se, Tretyakova lab 2-230
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| City |
Minneapolis |
| State/province |
Minnesota |
| ZIP/Postal code |
55455 |
| Country |
USA |
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| Platform ID |
GPL21626 |
| Series (2) |
| GSE163037 |
Multi-omics characterization of inflammatory bowel disease induced hyperplasia/dysplasia in the Rag2-/- / Il10-/- mouse model [RRBS] |
| GSE163038 |
Multi-omics characterization of inflammatory bowel disease induced hyperplasia/dysplasia in the Rag2-/- / Il10-/- mouse model |
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| Relations |
| BioSample |
SAMN17058527 |
| SRA |
SRX9673791 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4970534_5624_OXO_Sym.meth.txt.gz |
79.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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