|
| Status |
Public on May 29, 2024 |
| Title |
Female_PFC_BPA_RNA-seq rep3 |
| Sample type |
SRA |
| |
|
| Source name |
prefrontal cortex
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: prefrontal cortex
age: 4 months
Sex: female
treatment: BPA (40 ug/kg bw/day)
mouse id: 3625
|
| Treatment protocol |
Timed-pregnant C57BL/6Slac mice were randomly assigned into two groups, receiving either corn oil (Ctrl) or BPA (40 ug/kg bw/day) administered by oral gavage from gestational day 0.5 to 13.5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Prefrontal cortex were collected, flash frozen on dry ice, and RNA was harvested using RNeasy Lipid Tissue Mini Kit (Qiagen Cat. No. 74804). A total of 1 ug RNA was used for mRNA library preparation.
mRNA was captured by Oligo (dT) magnetic beads and the quality was evaluated on Agilent 2100 Bioanalyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
Raw data were first analyzed by FastQC for quality control
Reads were trimmed with Trim Galore (--quality 20 --phred33 --stringency 1 --length 20).
Clean data were aligned to the reference genome (UCSU, mm10) through HISAT2
SAMtools v1.6 were used to convert SAM files to BAM files, sort and build the alignment file index
FeatureCounts v1.6.3 from the Subread package was used for gene count with parameters set as: -t exon -g gene_id
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw counts for each Sample.
|
| |
|
| Submission date |
Nov 30, 2023 |
| Last update date |
May 29, 2024 |
| Contact name |
Yan Jiang |
| E-mail(s) |
yan_jiang@fudan.edu.cn
|
| Organization name |
Fudan University
|
| Department |
Institutes of Brain Science
|
| Street address |
131 Dongan rd
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL28457 |
| Series (2) |
| GSE249012 |
Epigenetic profiling in adult brain after prenatal BPA exposure [RNA-seq] |
| GSE249016 |
Epigenetic profiling in adult brain after prenatal BPA exposure |
|
| Relations |
| BioSample |
SAMN38510666 |
| SRA |
SRX22686682 |
