|
| Status |
Public on Oct 23, 2024 |
| Title |
BEC2F_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Sprague-Dawley Rat brain
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
tissue: brain
age: neonatal
Sex: female
genotype: wild-type
treatment: e-cig aerosol vapor
|
| Treatment protocol |
The first group was exposed to e_x0002_cigarette aerosol; and the 2nd group was exposed to air in the same chamber.
|
| Growth protocol |
Housed under a control temperature (22 ºC) and photoperiod (12-h light and 12-h dark cycle) with food and water ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The genomic DNA and total RNA extraction from the neonatal brain tissues were isolated with the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, USA).100 ng of total RNA and 100 ng of gDNA for each sample were used for the following sequence analysis.
RNA-seq libraries was constructed using the NuGEN Ovation universal RNA-seq kit (TECAN). RRBS libraries were constructed following standard protocols of the NuGEN Ovation Ultralow Methyl-seq Library Systems.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Raw RNA-seq fastq data was assessed for sequencing quality using FastQC
Adapters and primers were trimmed using Trimmomatic (v0.3.7).
Reads were aligned to the rat reference genome NCBI Rnor6.0, downloaded from iGenome, using Kallisto (v.0.44.0) with the default parameter settings.
The read counts matrix from Kallisto was input to DESeq2 (v.1.38.0) to identify differentially expressed genes (DEG).
The DEGs were identified by DESeq2 with the cutoff of log2FC > +/- 0.2, p-value < 0.005 and padj<0.1.
Assembly: For RRBS analysis, raw fastq reads were trimmed using TrimGalore (v.0.4.5) and Nugen RRBS trimming script (trimRRBSdiversityAdaptCustomers.py). After trimming, reads were aligned to the human reference genome (GRCh38) with Bismark54 by default parameter settings, and PCR duplicates were removed by Nugen script (nudup.py).
Supplementary files format and content: genome NCBI Rnor6.0
Supplementary files format and content: Sequenced approximately 25M reads/each.
|
| |
|
| Submission date |
Oct 04, 2024 |
| Last update date |
Oct 23, 2024 |
| Contact name |
daliao Xiao |
| E-mail(s) |
[email protected]
|
| Phone |
909-558-4325
|
| Organization name |
Loma Linda University
|
| Department |
center for perinatal biology
|
| Lab |
L1561
|
| Street address |
11234 Anderson st
|
| City |
Loma Linda |
| State/province |
California |
| ZIP/Postal code |
92350 |
| Country |
USA |
| |
|
| Platform ID |
GPL25029 |
| Series (1) |
| GSE278792 |
Maternal e-cigarette exposure alters DNA methylome, site-specific CpG and CH methylation, and transcriptomic signatures in the neonatal brain |
|
| Relations |
| BioSample |
SAMN44061644 |
| SRA |
SRX26290938 |
