GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

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