|
| Status |
Public on Sep 09, 2022 |
| Title |
HF female placenta RNA rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
Placenta
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Placenta
strain: C57BL/6J
developmental stage: E14.5
Sex: female
treatment: paternal high-fat diet
|
| Treatment protocol |
Male mice were fed either a control or a high-fat diet for 8-10 weeks starting at 6 weeks of age
|
| Extracted molecule |
total RNA |
| Extraction protocol |
E14.5 placentas were collected at necropsy and snap frozen in liquid nitrogen. RNA extraction was performed using Qiagen’s RNeasy Mini Kit following the manufacturer’s protocol.
Libraries were prepared for illumina sequencing, and samples were sequenced on the illumina NovaSeq 6000 platform with 100 bp paired-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were trimmed using Trim Galore (version 0.5.0, parameters: --paired --retain_unpaired --phred33 --length 70 -q 5 --stringency 1 -e 0.1) (Krueger, 2015). Trimmed reads were aligned to the Ensembl Genome Reference Consortium mouse reference 38 (GRCm38) primary assembly using hisat2 (version 2.1.0, parameters: -p 8 --dta) (Kim, Langmead and Salzberg, 2015). Aligned files with SAM format were converted to binary SAM format (BAM) and sorted by genomic position using SAMtools (version 1.9) (Li et al., 2009). Transcripts were assembled and gene abundances calculated using Stringtie (version 2.1.2, parameters: -p 8 -e -B -A) (Pertea et al., 2015).
Assembly: mm10
Supplementary files format and content: gtf files generated by Stringtie
|
| |
|
| Submission date |
Jun 30, 2022 |
| Last update date |
Sep 09, 2022 |
| Contact name |
Anne-Sophie Pépin |
| E-mail(s) |
anne-sophie.pepin@mail.mcgill.ca
|
| Organization name |
McGill University
|
| Department |
Department of Pharmacology and Therapeutics
|
| Street address |
21111 Lakeshore road
|
| City |
Sainte-Anne-de-Bellevue |
| State/province |
QC |
| ZIP/Postal code |
H9X3V9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE207313 |
Paternal obesity alters the sperm epigenome and and is associated with changes in the placental transcriptome and its cellular composition [RNA-seq] |
| GSE207326 |
Paternal obesity alters the sperm epigenome and and is associated with changes in the placental transcriptome and its cellular composition |
|
| Relations |
| BioSample |
SAMN29470596 |
| SRA |
SRX15959713 |
