|
| Status |
Public on Dec 05, 2023 |
| Title |
Adrenal Demedullated-IUGR Fetus 1 |
| Sample type |
SRA |
| |
|
| Source name |
Isolated Perirenal Adipose
|
| Organism |
Ovis aries |
| Characteristics |
internal animal id: 11-044-1
age (day in gestation): 135
Sex: M
weight at necropsy (kg): 2.26
|
| Treatment protocol |
IUGR fetuses were generated by exposing pregnant ewes to elevated ambient temperatures (40°C for 12h; 35°C for 12h; dew point 22°C) from 38 ± 1 days gestation age (dGA) until 94 ± 2 dGA. Control fetuses were from pregnant ewes that were maintained in a thermoneutral environment (22°C) and pair fed to the average daily dietary intake of the heat stressed ewes.
|
| Growth protocol |
Columbia-Rambouillet crossbred ewes carrying singleton pregnancies.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The entire perirenal adipose depot above the left kidney was removed, snap frozen in liquid nitrogen and stored at -80C for RNA extraction with Qiagen Microprep RNAeasy.
mRNA was selected and double-stranded cDNA libraries with ligated sequencing adapters was constructed with the Illumina TruSeq RNA Sample Prep Kit. Cluster generation was conducted with Illumina TruSeq 100bp PE (paired end) cluster kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Paired reads were filtered to remove reads less than 65 nt using Trimmomatic
Tophat 2.0.14 was used to map reads using parameters -a 20 -m 1 -I 10^5 -g 9 -N 3 --read-gap-length 1 --read-edit-dist 4 --read-realign-edit-dist 0 --library-type fr-unstranded
Cufflinks 2.2.1 was used to determine the transcriptome (annotation only) using parameters -G oar3174.gtf -b genome.fa -u -N -F 0.05
A unified non-redundant transcriptome (merge.gtf) was determined for all samples using Cuffmerge 2.2.1
Quantification of gene expression for all samples was determined using Cuffquant 2.2.1 with parameters -u -library-type fr-unstranded -b genome.fa -max-bundle-frags 10^7 merged.gtf
Cuffdiff 2.2.1 was used to determine statistical differences in gene expression between treatments using parameters -u -c 24 -FDR 0.05 -b genome.fa --max-bundle-frags 10^7 -compatible-hits-norm --library-type fr-unstranded merged.gtf
Genome_build: Genome Ensembl release 74 Ovis_aries.Oar_v3.1.dna_sm.toplevel.fa; annotation Ensembl Ovis_aries.Oar_v3.1.74.gtf
Supplementary_files_format_and_content: gene_exp.diff.gz: Tab separated values contains the gene level statistical analysis unmodified from Cuffdiff 2.2.1
Supplementary_files_format_and_content: gene.FPKM.tsv.gz: Tab separated values containing columns with tracking_id, gene_id and locus along with FPKM values for each treatment.
|
| |
|
| Submission date |
Jun 14, 2019 |
| Last update date |
Dec 05, 2023 |
| Contact name |
Sean W Limesand |
| E-mail(s) |
limesand@ag.arizona.edu
|
| Phone |
520-626-8903
|
| Organization name |
University of Ariziona
|
| Department |
Animal & Comparative Biomedical Sciences
|
| Lab |
Perinatal Biology Laboratory
|
| Street address |
4101 N Campbell Ave
|
| City |
Tucson |
| State/province |
AZ |
| ZIP/Postal code |
85719 |
| Country |
USA |
| |
|
| Platform ID |
GPL15670 |
| Series (1) |
| GSE132734 |
RNA Sequencing of Perirenal Adipose Tissue from Intrauterine Growth Restricted and Normally-Grown Near Term Sheep Fetuses with and without intact adrenal medulla. |
|
| Relations |
| BioSample |
SAMN12057770 |
| SRA |
SRX6071091 |
