|
| Status |
Public on Aug 22, 2022 |
| Title |
FPLGD15 |
| Sample type |
SRA |
| |
|
| Source name |
Placenta
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Placenta
Sex: Female
strain: C57BL/6
|
| Growth protocol |
Gestation day 15 of wildtype mice. The vaginal plug was observed was considered day 0.5 of gestation to detemine gestational age.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Freshly collected gestation day 15 placenta and fetal brain from littermate wildtype mice were snap frozen in liquid nitrogen. Genomic DNA was isolated from frozen specimen using
Genomic DNA was extracted using Gentra Puregene Tissue Kit (catalog #158667, Qiagen) from placenta and fetal brain of day 15 fetuses of both sexes from the wildtype mice (total 4 samples). Equimolar amount of DNA from three biological replicates for these samples. The pooled DNA was used for bisulfite conversion and libraries were prepared by the University of Missouri DNA core using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The raw sequence files were first chekced for quality by FASTQC.
The quality control was performed using cutadpat
Bismark tool 'bismark_genome_preparation' was used to process reference genome that is suitable for WGBS read mapping.
Bowtie2 was used for read aligment to processd genome sequences
The bismark toll 'bismark_methylation_extractor' tool was used to generate the coverage files for methylations.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Bismark coverage files of genome positions (1-based genomic genomic coordinates) with percentage and count of methylated and unmthylated reads for each sample. The columns represent <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>.
|
| |
|
| Submission date |
Sep 06, 2020 |
| Last update date |
Aug 24, 2022 |
| Contact name |
Susanta K. Behura |
| E-mail(s) |
behuras@missouri.edu
|
| Organization name |
Univeristy of Missouri
|
| Department |
Division of Animal Sciences
|
| Street address |
920 East Campus Drive
|
| City |
Columbia |
| State/province |
Missouri |
| ZIP/Postal code |
65211 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE157553 |
Fetal origin of sex-bias brain aging |
| GSE157556 |
Insights into the regulation of the brain-placental axis |
|
| Relations |
| BioSample |
SAMN16070425 |
| SRA |
SRX9084788 |
