|
| Status |
Public on Jul 17, 2021 |
| Title |
GD 135_Control_5114_Male |
| Sample type |
SRA |
| |
|
| Source name |
Placentome
|
| Organism |
Ovis aries |
| Characteristics |
treatment: Control
day: 135
Sex: Male
|
| Treatment protocol |
Control animals were fed 100% of their NRC nutritional requirements from Day 35 to Day 135 of pregnancy. Nutrient restricted animals were fed 50% of their NRC nutritional requirements for the same time period.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent, treated with DNAse I, and purified using an RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Libraries were multiplexed and sequenced from both directions as 75 base pair paired-end reads on one lane on a NextSeq500 instrument
Raw sequences (FASTQ) were subjected to quality check by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The program fqtrim (https://ccb.jhu.edu/software/fqtrim/) was used to remove adapters, perform quality trimming (phred score >30) by a sliding window scan (6 nucleotides) and select read length of 30 nucleotides or longer after trimming.
The reads obtained from the quality control step were mapped to the sheep reference genome (Oar_v3.1) by using Hisat2 aligner. The program FeatureCounts was used to quantify read counts by using the sequences alignment files of each sample.
Genes with evidence of expression (counts per million; rowSum >5) were used for model-based differential expression analysis using the edgeR robust method.
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: CSV file with genes by row and samples by column, raw counts
Supplementary_files_format_and_content: Matrix file with normalized CPM from edgeR for all samples
|
| |
|
| Submission date |
Jul 15, 2021 |
| Last update date |
Jul 17, 2021 |
| Contact name |
Michael Carey Satterfield |
| E-mail(s) |
csatterfield@tamu.edu
|
| Organization name |
Texas A&M University
|
| Department |
Animal Science
|
| Street address |
2471 TAMUS
|
| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
TX |
| Country |
USA |
| |
|
| Platform ID |
GPL22509 |
| Series (1) |
| GSE180182 |
Placental transcriptome adaptations to maternal nutrient restriction in sheep |
|
| Relations |
| BioSample |
SAMN20247373 |
