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Sample GSM3589437 Query DataSets for GSM3589437
Status Public on Feb 05, 2019
Title CSB+/- rep1
Sample type SRA
 
Source name CSB+/-_cerebellum
Organism Rattus norvegicus
Characteristics strain background: Sprague-Dawly (SD)
age: 10-week old age
genotype/variation: heterozygous mutant for CSB; CSBR571X/-
tissue: Cerebellum cortex
Extracted molecule total RNA
Extraction protocol Cerebellar cortex tissues were removed, flash frozen and homogenized in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description F1-1
Data processing FastQC was conducted for Quality control (QC) of RNA-seq reads
Trimming was performed by seqtk for known Illumina TruSeq adapter sequences, poor reads, and ribosomal RNA reads
Trimmed reads were mapped to the Rattus norvegicus reference genome by the Hisat 2(version:2.0.4)
String Tie(version:1.3.0) was performed for each gene count from trimmed reads
Gene counts were normalized by trimmed mean of M-values, and fragments per kilobase of transcript per million mapped reads (FPKM) in Perl script
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
 
Submission date Feb 04, 2019
Last update date Feb 12, 2019
Contact name Yuming Wang
E-mail(s) wangyuming2006@hotmail.com
Phone 008602037103555
Organization name Guangzhou medical university
Department School of Basic Medical Science
Street address Room 512, Anatomy Building
City Guangzhou
State/province Guangdong
ZIP/Postal code 511436
Country China
 
Platform ID GPL24688
Series (1)
GSE126032 Gloable gene expression is affected by loss of CSB function in the rat model for Cockayne syndrome
Relations
BioSample SAMN10868556
SRA SRX5329405

Supplementary file Size Download File type/resource
GSM3589437_F1-1.xlsx 2.1 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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