|
| Status |
Public on Sep 23, 2015 |
| Title |
NP-2 |
| Sample type |
SRA |
| |
|
| Source name |
thyroid collected from non-pregnant (NP) rats, repeat #2
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: thyroid
group: non-pregnant (NP) rats
strain: Sprague-Dawley
|
| Growth protocol |
Adult pregnant Sprague-Dawley rats and their non-pregnant controls were utilized in this study. Pregnant rats were obtained by co-caging two female rats with a male rat overnight. Success of mating was confirmed next morning by the presence of a vaginal plug. The day of the vaginal plug was designated as day 1 of pregnancy. Thyroid tissues were collected from non-pregnant (n = 3) rats and pregnant rats on days 8 (n=3), 12 (n=4) and 18 (n=3) of pregnancy. All collected tissues were then snap-frozen in liquid nitrogen and stored at -80 °C for further analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from thyroid samples was extracted using TRIzol reagent (invitrogen). RNA purity and integrity were assessed by using the ND-1000 Nanodrop and the Agilent 2200 TapeStation, respectively. The following parameters were set for RNA quality control: A260/A280 ratio ≥ 1.8, A260/A230 ratio ≥ 2.0 and RIN value ≥ 7.0. RNA-Seq libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer’s protocol. Finally, sequencing of the libraries was conducted on an Illumina HiSeq™ 2500 system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
mRNA(polyA+)
|
| Data processing |
A computational pipeline was used to process RNA-seq data. Sequence data were mapped to rat reference genome rn5 with Tophat v1.4.0 with default parameters. HTSeq-count was subsequently employed to convert aligned short reads into read counts for each gene model in the ENSEMBL database release 81. Differential expression between was assessed by DEseq using read counts as input. The Benjamini-Hochberg multiple test correction method was enabled. Differentially expressed genes were chosen according to the criteria of fold change > 2 and adjusted p-value < 0.05.
Genome_build: rn5
Supplementary_files_format_and_content: Tab-delimited text files include gene read count values for each sample. The first column is gene ID and the second column is gene name, and the 3rd column is read count value.
|
| |
|
| Submission date |
Sep 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ji-Long Liu |
| E-mail(s) |
[email protected]
|
| Organization name |
South China Agricultural University
|
| Street address |
483 Wushan Rd
|
| City |
Guangzhou |
| ZIP/Postal code |
510642 |
| Country |
China |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE73307 |
A transcriptomic study of maternal thyroid adaptation to pregnancy in rats |
|
| Relations |
| BioSample |
SAMN04100678 |
| SRA |
SRX1271847 |
