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Sample GSM6108643

Query DataSets for GSM6108643

Status

Public on May 18, 2023

Title

KO-d12C

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

this sample is actually WT-d12C sample, it was mislabeled
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