|
| Status |
Public on Sep 05, 2018 |
| Title |
09027: Saline-Control 2 |
| Sample type |
SRA |
| |
|
| Source name |
Isolated fetal pancreatic islets
|
| Organism |
Ovis aries |
| Characteristics |
tissue: Isolated fetal pancreatic islets
gestational age (days): 139
fetal sex: female
fetal weight (kg): 3.6
|
| Treatment protocol |
Control fetuses received an intravenous infusion of diluent (0.3% ascorbic acid in 0.9% saline). NE fetuses received an intravenous infusion of NE (Norepinephrine Bitartrate, Bedford Labs) for 7 days at preset rates for each day of treatment (day 1 at 1 µg/min, days 2-4 at 2 µg/min, and days 5-7 at 4µg/min).
|
| Growth protocol |
Columbia-Rambouillet crossbred ewes carrying singleton pregnancies.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Islets were isolated and handpicked then frozen 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 2500 |
| |
|
| Description |
09-027
|
| Data processing |
Tophat (v2.0.1) -a 15 -m 1 -I 50000 -g 9 -N 3 -rgl 4 --red 7 -rred 0
cufflinks (v2.1.1) -G -b oar3174.fa -u -N -F 0.05 Annotation- Ensembl Ovis_aries.Oar_v3.1.74.gtf
cuffmerge -G
cuffdiff -N -u -c 24 --library-type fr-unstranded -b oar3174.fa --max-bundle-frags 25000000
Genome_build: Ensemble release 74 Ovis_aries.Oar_v3.1.dna_sm.toplevel.fa.gz
Supplementary_files_format_and_content: gene_exp.diff - cuffdiff gene level statistics
Supplementary_files_format_and_content: gene_id.repFPKM.txt - table of gene ID, locus and FPKM values from cuffdiff genes.FPKM_tracking
|
| |
|
| Submission date |
Nov 02, 2017 |
| Last update date |
May 15, 2019 |
| 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 |
GPL19778 |
| Series (1) |
| GSE106440 |
RNAseq of Islets Isolated from Near Term Fetal Sheep after 7-day Infusion of Norepinephrine or Vehicle Control |
|
| Relations |
| BioSample |
SAMN07967135 |
| SRA |
SRX3353293 |
