|
Status |
Public on Dec 05, 2023 |
Title |
Sham-IUGR Fetus 3 |
Sample type |
SRA |
|
|
Source name |
Isolated Perirenal Adipose
|
Organism |
Ovis aries |
Characteristics |
internal animal id: 12-026-1 age (day in gestation): 134 Sex: M weight at necropsy (kg): 1.69
|
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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
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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.
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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 |
SAMN12057772 |
SRA |
SRX6071089 |