|
| Status |
Public on Jan 19, 2023 |
| Title |
Mouse_JF1xC57BL/6_Epiblast_rep1 [JxC_EB1] |
| Sample type |
SRA |
| |
|
| Source name |
epiblast
|
| Organism |
Mus musculus |
| Characteristics |
strain: F1 hybrid resulting from female JF1/Ms and male C57BL/6N mice
age: embryonic days 7.25
genotype: wild type
cell type: epiblast
Sex: female
|
| Treatment protocol |
E8.5 F1 hybrid rat embryos were isolated from reciprocally crossing BN/CrlCrlj (BN rat) and WKY/NCrlCrlj (WKY rat) strains. E7.25 F1 hybrid mouse embryos were isolated from reciprocally crossing C57BL/6N and JF1/Ms strains. For both rat and mouse embryos, the ectoplacental cone (EPC) was dissected from the rest of the embryo before removing the visceral endoderm. Finally, the epiblast (EB) was dissected from the extraembryonic ectoderm (ExE). Each ExE lysate was used for rapid genetic sex determination by direct PCR amplification of the Y chromosome gene using specific primers for mouse Zfy and rat Sry. Only female EBs and EPCs were subjected to whole genome bisulphite sequencing.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using AllPrep DNA/RNA Micro Kit (Qiagen) according to manufacturer’s protocols.
One hundred nanograms of genomic DNA from JF1 (female) and C57BL/6 (male) mouse hybrids were prepared for Methyl-seq (Illumina) library construction. Twenty nanograms of genomic DNA from the other mouse and rat hybrid crosses were prepared for rPBAT or tPBAT library construction.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
WGBS (Illumina's TruSeq DNA Methylation Kit)
mouse_epiblast_maternal_rep1-3_x1.bw
mouse_epiblast_maternal_rep1-3_x5.bw
mouse_epiblast_paternal_rep1-3_x1.bw
mouse_epiblast_paternal_rep1-3_x5.bw
|
| Data processing |
>Sequencing reads were trimmed using Trimmomatic (v0.32) and the following parameters: SLIDINGWINDOW:3:10 MINLEN:36 ILLUMINACLIP:TruSeq2-3-PE.fa:2:30:10.
>Read pairs that survived trimming were aligned to diploid rat or mouse pseudogenomes using MEA and Bismark.
>Duplicate reads were removed and the number of methylated and unmethylated reads overlapping each CpG of the rat or mouse genome was reported. This resulted in total (allele-agnostic), maternal- and paternal-specific CpG report files.
>Replicates and reciprocal crosses were merged for visualization and analyses.
>CpGs covered by at least 5 (total) or 1 (maternal or paternal) sequencing reads were assessed for methylation levels and genome-wide tracks were sunsequently generated for visualization.
Genome_build: rn6
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files for each sample
|
| |
|
| Submission date |
Oct 24, 2021 |
| Last update date |
Jan 19, 2023 |
| Contact name |
Hisato Kobayashi |
| E-mail(s) |
hiskobay@naramed-u.ac.jp
|
| Phone |
+81-744-29-8015
|
| Organization name |
Nara Medical University
|
| Department |
Department of Embryology
|
| Street address |
840 Shijo-Cho
|
| City |
Kashihara |
| State/province |
Nara |
| ZIP/Postal code |
634-8521 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE186492 |
Rat and mouse imprintomes (allele-specific DNA methylomes) |
|
| Relations |
| BioSample |
SAMN22550073 |
| SRA |
SRX12757165 |
