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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 12, 2017 |
| Title |
J-29 EGC |
| Sample type |
SRA |
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| Source name |
EGC
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| Organism |
Mus musculus |
| Characteristics |
sex chromosomes: XX
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
generation protocol: Genital ridges containing primordial germ cells (PGCs) were retrieved from E11.5/12.5 mouse embryos. PGCs were collected from the genital ridges by trypsinization and centrifugation. Subsequently, isolated PGCs were cultured on stem cell factor (SCF)-secreting MEF feeder containing 2i-LIF medium (Ying et al., 2008) supplemeted with 60 ng/ml exogenous SCF and 10 ng/ml bFGF. The cells were cultured for 3 days without changing medium. After that, the cells were cultured for additional 7-11 days and fed every other day with fresh 2i-LIF medium until picking. Outgrowth from the culture was picked, trypsinized, and re-plated onto MEF feeders containing KO DMEM (Invitrogen) supplemented with 15% FBS (Hyclone), 1mM L- glutamine, 100 uM MEM non-essential amino acids, and 0.1 mM beta-mercaptoethanol, and LIF.
Genomic DNA was collected using phenol/chloroform extraction
mRRBS libraries were prepared as previously described (Boyle et al. 2012). Briefly, genomic sequences were digested using the MspI restriction enzyme, which cuts at the sequence CCGG. Digested fragments were subjected to bisulfite treatment which converts unmethylated cytosine residues to uracil
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
E11.5 EGC (XX)
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| Data processing |
Alignment: bisulfite-converted reads were aligned to a MspI-digested mm9 mouse genome using MAQ in bisulfite alignment mode using the following parameters: -D -s 0 -M c -e 100
Methylation calling: CpGs in the reference sequence were compared to the sequence in the aligned read. If bisulfite conversion (signifying an unmethylated cytosine) was detected, the read added to the unmethylated count for that CpG, otherwise, it added to the methylated count.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files contain the number of methylated and total reads for CpGs covered by RRBS
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| Submission date |
May 11, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kendell Clement |
| Organization name |
Harvard University
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| Lab |
Meissner Lab
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| Street address |
7 Divinity Ave.
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE68733 |
DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells |
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| Relations |
| BioSample |
SAMN03651951 |
| SRA |
SRX1023078 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1679868_E11-5_EGC_XX_2.bed.gz |
10.8 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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