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Sample GSM6108653 Query DataSets for GSM6108653
Status Public on May 18, 2023
Title MWJ-3
Sample type SRA
 
Source name rat junctional zone
Organism Rattus norvegicus
Characteristics gestation day: 14.5
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from cells and tissues using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits (Illumina, San Diego, CA). Barcoded cDNA libraries were multiplexed and sequenced with a HiSeq2000 DNA sequencer (100-bp paired-end reads) using a TruSeq 200-cycle SBS kit (Illumina) at the KUMC Genome Sequencing Facility. Reads from *.fastq files were mapped to the rat reference genome (Rnor_6.0) using CLC Genomics Workbench 20.0.4 (Qiagen, Redwood City, CA). mRNA abundance was expressed in reads per kb of exon per million reads mapped. A false discovery rate of 0.05 was used as a cutoff for significant differential expression (wild type versus null).
RACE
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection RACE
Instrument model Illumina NovaSeq 6000
 
Description Holtzman Sprague-Dawley rats were housed in an environmentally controlled facility at the University of Kansas Medical Center (KUMC) with lights on from 0600 to 2000 h and allowed free access to food and water. Female rats (8-10 weeks of age) were mated with adult male rats (>3 months of age). Mating was assessed by inspection of vaginal lavages. ­The presence of sperm in the vagina was designated gd 0.5. Placentation sites were dissected on gestation day 12.5 and placental discs were isolated. Dissected placental disc tissues were snap-frozen in liquid nitrogen and stored at -80°C until processing for RNA isolation. Total RNA was isolated from tissues using TRIzol reagent (Thermo Fisher Scientific, catalog No. 15596018). All rats were maintained in accordance with institutional policies for the care and use of vertebrate animals in research using protocols approved by the KUMC Animal Care and Use Committee.
Data processing Reads from *.fastq files were mapped to the rat reference genome (Rnor_6.0) using CLC Genomics Workbench 20.0.4 (Qiagen, Redwood City, CA).
mRNA abundance was expressed in reads per kb of exon per million reads mapped.
A false discovery rate of 0.05 was used as a cutoff for significant differential expression.
Functional patterns of transcript expression were analyzed using Ingenuity Pathway Analysis (Qiagen).
Assembly: rat reference genome (Rnor_6.0)
 
Submission date May 05, 2022
Last update date May 18, 2023
Contact name Khursheed Iqbal
E-mail(s) kiqbal@kumc.edu
Phone 913 588 5690
Organization name University of Kansas Medical Center
Department Pathology
Street address 3901 Rainbow Blvd
City Kansas City
State/province Kansas
ZIP/Postal code 66160
Country USA
 
Platform ID GPL25947
Series (2)
GSE202338 CITED2 is a conserved regulator of deep placentation (Rat II)
GSE202339 CITED2 is a conserved regulator of deep placentation
Relations
BioSample SAMN28103355
SRA SRX15168856

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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