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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 24, 2015 |
| Title |
MommeD28/MommeD28 mutant E10.5 embryo rep2 |
| Sample type |
SRA |
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| Source name |
E10.5 embryo rep2
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| Organism |
Mus musculus |
| Characteristics |
strain: FVB
genotype/variation: MommeD28/MommeD28 mutant
gender: Male
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| Treatment protocol |
N/A
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| Growth protocol |
N/A
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen AllPrep
Illumina
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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 |
3' ends were trimmed for low quality bases using trim_seq with the settings (www.biopieces.org)
Reads were mapped to the mouse genome (build mm9) using Bismark and Bowtie2 with the options -N 1 -D 30
PCR duplicates were removed from mapped reads using deduplicate_bismark_alignment_output.pl
Methylation values extracted using bismark_methylation_extractor with the setttings --ignore_r2 2
CpG methylation values were finally merged into a single value per CpG
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph showing %mCG. Additionally, columns with counts for unconverted Cs and converted Cs are included.
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| Submission date |
May 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Harald Oey |
| Organization name |
La Trobe University
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| Department |
Genetics
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| Street address |
Kingsbury Drive
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| City |
Bundoora |
| State/province |
Vic |
| ZIP/Postal code |
3086 |
| Country |
Australia |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE58108 |
Rlf, a widely-spaced zinc finger protein, is involved in maintaining epigenetic marks at CpG island shores and enhancer elements across the genome |
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| Relations |
| BioSample |
SAMN02803954 |
| SRA |
SRX555624 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1400927_E10.5_embryo_Rlf_KO_rep2.tab.gz |
146.6 Mb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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