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Sample GSM6108644 Query DataSets for GSM6108644
Status Public on May 18, 2023
Title WT-d12A
Sample type SRA
 
Source name rat trophoblast stem cells
Organism Rattus norvegicus
Characteristics cell type: trophoblast cell
strain: Holtzman Sprague-Dawley
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 (null versus wild type).
RACE
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection RACE
Instrument model Illumina NovaSeq 6000
 
Description Rat TS cells were maintained in stem state medium (RPMI-1640 containing 20% FBS, 50 µm 2-mercaptoethanol, 1 mM sodium pyruvate, 100 µm penicilin and streptomycin, 25 ng/ml fibroblast growth factor 4, 1 µg/ml heparin and 70% embrynic fibroblast-conditioned medium. Differentiation was induced by the removal of FGF4, heparin and embrynic fibroblast-conditioned medium, and cells were cultured in RPMI medium containing 1% FBS for 12 days.
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)
GSE202337 CITED2 is a conserved regulator of deep placentation (Rat I)
GSE202339 CITED2 is a conserved regulator of deep placentation
Relations
BioSample SAMN28103384
SRA SRX15168702

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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