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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 13, 2018 |
| Title |
Dnmt1 KO Jejunum |
| Sample type |
SRA |
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| Source name |
Jejunum
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| Organism |
Mus musculus |
| Characteristics |
sample: smMHCCre-eGFP/+;Dnmt1-/-
strain: C57BL/6
genotype/variation: B6.Cg-Tg(Myh11-cre,-EGFP)2Mik/J;Dnmt1lox/lox
tissue: Jejunum smooth muscle
age: 15 days
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
AllPrep DNA Spin Column
Methyl-MidiSeq® libraries were prepared from 300 ng of genomic DNA digested with 40 units of BfaI, 40 units of MseI, and 80 units of MspI and the fragments produced were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine. Adapter-ligated fragments were filled in and 3’-terminal-A extended, then purified using the Zymo Research (ZR) DNA Clean & ConcentratorTM – 5 kit (Cat#: D4003). Bisulfite treatment of the fragments was done using the EZ DNA Methylation – Lightning kit (ZR, Cat#: D5030). PCR was performed and the size and concentration of the fragments were confirmed on the Agilent 2200 TapeStation, then sequenced on the Illumina Hiseq with 50 bp PE parameters.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Raw data files had their adapters removed using trim_galore, quality trimming was also done, reads shorter than 20 bp were discarded
Pre-processed fastq files were aligned to human hg19 using bismark
Methylation calling was done on the bamfiles to create browser tracks for CpG, CHG, and CHH sites for each sample, these are in bigbed format
Genome_build: mm10
Supplementary_files_format_and_content: bigbed, browser tracks that contain methylation count and total count of reads per site
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| Submission date |
Jan 25, 2018 |
| Last update date |
Feb 13, 2018 |
| Contact name |
Seungil Ro |
| E-mail(s) |
sro@medicine.nevada.edu
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| Phone |
775-784-1462
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| Organization name |
University of Nevada School of Medicine
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| Department |
Physiology and Cell Biology
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| Street address |
1664 North Virginia St
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| City |
Reno |
| State/province |
NV |
| ZIP/Postal code |
89557 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE109274 |
DNA methylation, through DNMT1, has an essential role in the development of gastrointestinal smooth muscle cells and disease |
| GSE109641 |
DNA methylation, through DNMT1, has an essential role in the development of gastrointestinal smooth muscle cells and disease (BiSulfite-seq) |
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| Relations |
| BioSample |
SAMN08395453 |
| SRA |
SRX3599602 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2947784_Dnmt1_KO_CHG_meth.bb |
493.5 Mb |
(ftp)(http) |
BB |
| GSM2947784_Dnmt1_KO_CHH_meth.bb |
1.4 Gb |
(ftp)(http) |
BB |
| GSM2947784_Dnmt1_KO_CpG_meth.bb |
196.1 Mb |
(ftp)(http) |
BB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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